retrieve_ensembl_bed: bedutil.py annotate

annotate bedutil.py @ 2:e385fe93df68 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"

author	galaxyp
date	Mon, 07 Oct 2019 16:14:19 -0400
parents	c3d600729b6f
children

rev	line source
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	1 #!/usr/bin/env python
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	2 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	3 #
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	4 #------------------------------------------------------------------------------
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	5 # University of Minnesota
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	6 # Copyright 2016, Regents of the University of Minnesota
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	7 #------------------------------------------------------------------------------
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	8 # Author:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	9 #
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	10 # James E Johnson
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	11 #
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	12 #------------------------------------------------------------------------------
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	13 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	14
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	15 from __future__ import print_function
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	16
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	17 import sys
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	18
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	19 from Bio.Seq import reverse_complement, translate
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	20
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	21
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	22 def bed_from_line(line, ensembl=False, seq_column=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	23 fields = line.rstrip('\r\n').split('\t')
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	24 if len(fields) < 12:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	25 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	26 (chrom, chromStart, chromEnd, name, score, strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	27 thickStart, thickEnd, itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	28 blockCount, blockSizes, blockStarts) = fields[0:12]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	29 bed_entry = BedEntry(chrom=chrom, chromStart=chromStart, chromEnd=chromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	30 name=name, score=score, strand=strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	31 thickStart=thickStart, thickEnd=thickEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	32 itemRgb=itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	33 blockCount=blockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	34 blockSizes=blockSizes.rstrip(','),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	35 blockStarts=blockStarts.rstrip(','))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	36 if seq_column is not None and -len(fields) <= seq_column < len(fields):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	37 bed_entry.seq = fields[seq_column]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	38 if ensembl and len(fields) >= 20:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	39 bed_entry.second_name = fields[12]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	40 bed_entry.cds_start_status = fields[13]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	41 bed_entry.cds_end_status = fields[14]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	42 bed_entry.exon_frames = fields[15].rstrip(',')
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	43 bed_entry.biotype = fields[16]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	44 bed_entry.gene_name = fields[17]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	45 bed_entry.second_gene_name = fields[18]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	46 bed_entry.gene_type = fields[19]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	47 return bed_entry
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	48
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	49
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	50 def as_int_list(obj):
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	51 if obj is None:
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	52 return None
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	53 if isinstance(obj, list):
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	54 return [int(x) for x in obj]
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	55 elif isinstance(obj, str):
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	56 return [int(x) for x in obj.split(',')]
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	57 else: # python2 unicode?
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	58 return [int(x) for x in str(obj).split(',')]
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	59
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	60
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	61 class BedEntry(object):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	62 def __init__(self, chrom=None, chromStart=None, chromEnd=None,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	63 name=None, score=None, strand=None,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	64 thickStart=None, thickEnd=None, itemRgb=None,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	65 blockCount=None, blockSizes=None, blockStarts=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	66 self.chrom = chrom
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	67 self.chromStart = int(chromStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	68 self.chromEnd = int(chromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	69 self.name = name
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	70 self.score = int(score) if score is not None else 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	71 self.strand = '-' if str(strand).startswith('-') else '+'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	72 self.thickStart = int(thickStart) if thickStart else self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	73 self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	74 self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	75 self.blockCount = int(blockCount)
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	76 self.blockSizes = as_int_list(blockSizes)
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	77 self.blockStarts = as_int_list(blockStarts)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	78 self.second_name = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	79 self.cds_start_status = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	80 self.cds_end_status = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	81 self.exon_frames = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	82 self.biotype = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	83 self.gene_name = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	84 self.second_gene_name = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	85 self.gene_type = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	86 self.seq = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	87 self.cdna = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	88 self.pep = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	89 # T26C
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	90 self.aa_change = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	91 # p.Trp26Cys g.<pos><ref>><alt> # g.1304573A>G
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	92 self.variants = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	93
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	94 def __str__(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	95 return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s' % (
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	96 self.chrom, self.chromStart, self.chromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	97 self.name, self.score, self.strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	98 self.thickStart, self.thickEnd, str(self.itemRgb), self.blockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	99 ','.join([str(x) for x in self.blockSizes]),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	100 ','.join([str(x) for x in self.blockStarts]))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	101
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	102 def get_splice_junctions(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	103 splice_juncs = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	104 for i in range(self.blockCount - 1):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	105 splice_junc = "%s:%d_%d"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	106 % (self.chrom,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	107 self.chromStart + self.blockSizes[i],
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	108 self.chromStart + self.blockStarts[i+1])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	109 splice_juncs.append(splice_junc)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	110 return splice_juncs
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	111
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	112 def get_exon_seqs(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	113 if not self.seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	114 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	115 exons = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	116 for i in range(self.blockCount):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	117 exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	118 + self.blockSizes[i]])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	119 if self.strand == '-': # reverse complement
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	120 exons.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	121 for i, s in enumerate(exons):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	122 exons[i] = reverse_complement(s)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	123 return exons
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	124
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	125 def get_spliced_seq(self, strand=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	126 if not self.seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	127 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	128 seq = ''.join(self.get_exon_seqs())
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	129 if strand and self.strand != strand:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	130 seq = reverse_complement(seq)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	131 return seq
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	132
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	133 def get_cdna(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	134 if not self.cdna:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	135 self.cdna = self.get_spliced_seq()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	136 return self.cdna
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	137
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	138 def get_cds(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	139 cdna = self.get_cdna()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	140 if cdna:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	141 if self.chromStart == self.thickStart\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	142 and self.chromEnd == self.thickEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	143 return cdna
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	144 pos = [self.cdna_offset_of_pos(self.thickStart),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	145 self.cdna_offset_of_pos(self.thickEnd)]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	146 if 0 <= min(pos) <= max(pos) <= len(cdna):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	147 return cdna[min(pos):max(pos)]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	148 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	149
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	150 def set_cds(self, cdna_start, cdna_end):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	151 cdna_len = sum(self.blockSizes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	152 if 0 <= cdna_start < cdna_end <= cdna_len:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	153 cds_pos = [self.pos_of_cdna_offet(cdna_start),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	154 self.pos_of_cdna_offet(cdna_end)]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	155 if all(cds_pos):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	156 self.thickStart = min(cds_pos)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	157 self.thickEnd = max(cds_pos)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	158 return self
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	159 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	160
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	161 def trim_cds(self, basepairs):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	162 if self.chromStart <= self.thickStart < self.thickEnd <= self.chromEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	163 cds_pos = [self.cdna_offset_of_pos(self.thickStart),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	164 self.cdna_offset_of_pos(self.thickEnd)]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	165 if basepairs > 0:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	166 return self.set_cds(min(cds_pos) + basepairs, max(cds_pos))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	167 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	168 return self.set_cds(min(cds_pos), max(cds_pos) + basepairs)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	169 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	170
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	171 def get_cds_bed(self):
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	172 cds_pos = [self.cdna_offset_of_pos(self.thickStart),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	173 self.cdna_offset_of_pos(self.thickEnd)]
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	174 return self.trim(min(cds_pos), max(cds_pos))
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	175
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	176 def get_cigar(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	177 cigar = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	178 r = range(self.blockCount)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	179 xl = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	180 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	181 if xl is not None:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	182 intronSize = abs(self.blockStarts[x] - self.blockSizes[xl]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	183 - self.blockStarts[xl])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	184 cigar += '%dN' % intronSize
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	185 cigar += '%dM' % self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	186 xl = x
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	187 return cigar
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	188
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	189 def get_cigar_md(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	190 cigar = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	191 md = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	192 r = range(self.blockCount)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	193 xl = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	194 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	195 if xl is not None:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	196 intronSize = abs(self.blockStarts[x] - self.blockSizes[xl]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	197 - self.blockStarts[xl])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	198 cigar += '%dN' % intronSize
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	199 cigar += '%dM' % self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	200 xl = x
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	201 md = '%d' % sum(self.blockSizes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	202 return (cigar, md)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	203
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	204 def get_translation(self, sequence=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	205 translation = None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	206 seq = sequence if sequence else self.get_spliced_seq()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	207 if seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	208 seqlen = len(seq) / 3 * 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	209 if seqlen >= 3:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	210 translation = translate(seq[:seqlen])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	211 return translation
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	212
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	213 def get_translations(self):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	214 translations = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	215 seq = self.get_spliced_seq()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	216 if seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	217 for i in range(3):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	218 translation = self.get_translation(sequence=seq[i:])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	219 if translation:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	220 translations.append(translation)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	221 return translations
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	222
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	223 def pos_of_cdna_offet(self, offset):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	224 if offset is not None and 0 <= offset < sum(self.blockSizes):
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	225 r = list(range(self.blockCount))
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	226 rev = self.strand == '-'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	227 if rev:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	228 r.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	229 nlen = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	230 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	231 if offset < nlen + self.blockSizes[x]:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	232 if rev:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	233 return self.chromStart + self.blockStarts[x]\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	234 + self.blockSizes[x] - (offset - nlen)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	235 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	236 return self.chromStart + self.blockStarts[x]\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	237 + (offset - nlen)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	238 nlen += self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	239 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	240
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	241 def cdna_offset_of_pos(self, pos):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	242 if not self.chromStart <= pos < self.chromEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	243 return -1
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	244 r = list(range(self.blockCount))
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	245 rev = self.strand == '-'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	246 if rev:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	247 r.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	248 nlen = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	249 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	250 bStart = self.chromStart + self.blockStarts[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	251 bEnd = bStart + self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	252 if bStart <= pos < bEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	253 return nlen + (bEnd - pos if rev else pos - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	254 nlen += self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	255
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	256 def apply_variant(self, pos, ref, alt):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	257 pos = int(pos)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	258 if not ref or not alt:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	259 print("variant requires ref and alt sequences", file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	260 return
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	261 if not self.chromStart <= pos <= self.chromEnd:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	262 print("variant not in entry %s: %s %d < %d < %d" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	263 (self.name, self.strand,
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	264 self.chromStart, pos, self.chromEnd),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	265 file=sys.stderr)
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	266 print("%s" % str(self), file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	267 return
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	268 if len(ref) != len(alt):
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	269 print("variant only works for snp: %s %s" % (ref, alt),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	270 file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	271 return
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	272 if not self.seq:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	273 print("variant entry %s has no seq" % self.name, file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	274 return
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	275 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	276 if self.strand == '-':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	277 ref = reverse_complement(ref)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	278 alt = reverse_complement(alt)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	279 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	280 bases = list(self.seq)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	281 offset = pos - self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	282 for i in range(len(ref)):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	283 # offset = self.cdna_offset_of_pos(pos+i)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	284 if offset is not None:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	285 bases[offset+i] = alt[i]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	286 else:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	287 print("variant offset %s: %s %d < %d < %d" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	288 (self.name, self.strand, self.chromStart,
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	289 pos+1, self.chromEnd), file=sys.stderr)
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	290 print("%s" % str(self), file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	291 self.seq = ''.join(bases)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	292 self.variants.append("g.%d%s>%s" % (pos+1, ref, alt))
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	293
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	294 def get_variant_bed(self, pos, ref, alt):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	295 pos = int(pos)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	296 if not ref or not alt:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	297 print("variant requires ref and alt sequences", file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	298 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	299 if not self.chromStart <= pos <= self.chromEnd:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	300 print("variant not in entry %s: %s %d < %d < %d" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	301 (self.name, self.strand,
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	302 self.chromStart, pos, self.chromEnd),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	303 file=sys.stderr)
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	304 print("%s" % str(self), file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	305 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	306 if not self.seq:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	307 print("variant entry %s has no seq" % self.name, file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	308 return None
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	309 tbed = BedEntry(chrom=self.chrom,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	310 chromStart=self.chromStart, chromEnd=self.chromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	311 name=self.name, score=self.score, strand=self.strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	312 thickStart=self.chromStart, thickEnd=self.chromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	313 itemRgb=self.itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	314 blockCount=self.blockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	315 blockSizes=self.blockSizes,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	316 blockStarts=self.blockStarts)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	317 bases = list(self.seq)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	318 offset = pos - self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	319 tbed.seq = ''.join(bases[:offset] + list(alt)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	320 + bases[offset+len(ref):])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	321 if len(ref) != len(alt):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	322 diff = len(alt) - len(ref)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	323 rEnd = pos + len(ref)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	324 # need to adjust blocks
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	325 # change spans blocks,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	326 for x in range(tbed.blockCount):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	327 bStart = tbed.chromStart + tbed.blockStarts[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	328 bEnd = bStart + tbed.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	329 # change within a block or extends (last block)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	330 # adjust blocksize
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	331 # seq: GGGcatGGG
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	332 # ref c alt tag: GGGtagatGGG
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	333 # ref cat alt a: GGGaGGG
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	334 if bStart <= pos < rEnd < bEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	335 tbed.blockSizes[x] += diff
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	336 return tbed
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	337
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	338 # (start, end)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	339 def get_subrange(self, tstart, tstop, debug=False):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	340 chromStart = self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	341 chromEnd = self.chromEnd
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	342 if debug:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	343 print("%s" % (str(self)), file=sys.stderr)
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	344 r = list(range(self.blockCount))
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	345 if self.strand == '-':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	346 r.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	347 bStart = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	348 bEnd = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	349 for x in r:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	350 bEnd = bStart + self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	351 if bStart <= tstart < bEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	352 if self.strand == '+':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	353 chromStart = self.chromStart + self.blockStarts[x] +\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	354 (tstart - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	355 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	356 chromEnd = self.chromStart + self.blockStarts[x] +\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	357 self.blockSizes[x] - (tstart - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	358 if bStart <= tstop < bEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	359 if self.strand == '+':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	360 chromEnd = self.chromStart + self.blockStarts[x] +\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	361 (tstop - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	362 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	363 chromStart = self.chromStart + self.blockStarts[x] +\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	364 self.blockSizes[x] - (tstop - bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	365 if debug:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	366 print("%3d %s\t%d\t%d\t%d\t%d\t%d\t%d" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	367 (x, self.strand, bStart, bEnd,
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	368 tstart, tstop, chromStart, chromEnd), file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	369 bStart += self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	370 return(chromStart, chromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	371
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	372 # get the blocks for sub range
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	373 def get_blocks(self, chromStart, chromEnd):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	374 tblockCount = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	375 tblockSizes = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	376 tblockStarts = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	377 for x in range(self.blockCount):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	378 bStart = self.chromStart + self.blockStarts[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	379 bEnd = bStart + self.blockSizes[x]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	380 if bStart > chromEnd:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	381 break
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	382 if bEnd < chromStart:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	383 continue
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	384 cStart = max(chromStart, bStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	385 tblockStarts.append(cStart - chromStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	386 tblockSizes.append(min(chromEnd, bEnd) - cStart)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	387 tblockCount += 1
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	388 return (tblockCount, tblockSizes, tblockStarts)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	389
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	390 def trim(self, tstart, tstop, debug=False):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	391 (tchromStart, tchromEnd) =\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	392 self.get_subrange(tstart, tstop, debug=debug)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	393 (tblockCount, tblockSizes, tblockStarts) =\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	394 self.get_blocks(tchromStart, tchromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	395 tbed = BedEntry(
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	396 chrom=self.chrom, chromStart=tchromStart, chromEnd=tchromEnd,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	397 name=self.name, score=self.score, strand=self.strand,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	398 thickStart=tchromStart, thickEnd=tchromEnd, itemRgb=self.itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	399 blockCount=tblockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	400 blockSizes=tblockSizes, blockStarts=tblockStarts)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	401 if self.seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	402 ts = tchromStart-self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	403 te = tchromEnd - tchromStart + ts
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	404 tbed.seq = self.seq[ts:te]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	405 return tbed
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	406
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	407 def get_filtered_translations(self, untrimmed=False, filtering=True,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	408 ignore_left_bp=0, ignore_right_bp=0,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	409 debug=False):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	410 translations = [None, None, None]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	411 seq = self.get_spliced_seq()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	412 ignore = (ignore_left_bp if self.strand == '+'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	413 else ignore_right_bp) / 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	414 block_sum = sum(self.blockSizes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	415 exon_sizes = [x for x in self.blockSizes]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	416 if self.strand == '-':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	417 exon_sizes.reverse()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	418 splice_sites = [sum(exon_sizes[:x]) / 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	419 for x in range(1, len(exon_sizes))]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	420 if debug:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	421 print("splice_sites: %s" % splice_sites, file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	422 junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	423 if seq:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	424 for i in range(3):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	425 translation = self.get_translation(sequence=seq[i:])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	426 if translation:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	427 tstart = 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	428 tstop = len(translation)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	429 offset = (block_sum - i) % 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	430 if debug:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	431 print("frame: %d\ttstart: %d tstop: %d " +
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	432 "offset: %d\t%s" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	433 (i, tstart, tstop, offset, translation),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	434 file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	435 if not untrimmed:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	436 tstart = translation.rfind('*', 0, junc) + 1
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	437 stop = translation.find('*', junc)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	438 tstop = stop if stop >= 0 else len(translation)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	439 offset = (block_sum - i) % 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	440 trimmed = translation[tstart:tstop]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	441 if debug:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	442 print("frame: %d\ttstart: %d tstop: %d " +
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	443 "offset: %d\t%s" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	444 (i, tstart, tstop, offset, trimmed),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	445 file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	446 if filtering and tstart > ignore:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	447 continue
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	448 # get genomic locations for start and end
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	449 if self.strand == '+':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	450 chromStart = self.chromStart + i + (tstart * 3)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	451 chromEnd = self.chromEnd - offset\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	452 - (len(translation) - tstop) * 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	453 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	454 chromStart = self.chromStart + offset\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	455 + (len(translation) - tstop) * 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	456 chromEnd = self.chromEnd - i - (tstart * 3)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	457 # get the blocks for this translation
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	458 (tblockCount, tblockSizes, tblockStarts) =\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	459 self.get_blocks(chromStart, chromEnd)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	460 translations[i] = (chromStart, chromEnd, trimmed,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	461 tblockCount, tblockSizes, tblockStarts)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	462 if debug:
1 c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	463 print("tblockCount: %d tblockStarts: %s " +
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	464 "tblockSizes: %s" %
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	465 (tblockCount, tblockStarts, tblockSizes),
c3d600729b6f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1 galaxyp parents: 0 diff changeset	466 file=sys.stderr)
0 887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	467 return translations
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	468
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	469 def get_seq_id(self, seqtype='unk:unk', reference='', frame=None):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	470 # Ensembl fasta ID format
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	471 # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	472 # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	473 # gene:ENSG00000158815:transcript:ENST00000328693\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	474 # gene_biotype:protein_coding transcript_biotype:protein_coding
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	475 frame_name = ''
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	476 chromStart = self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	477 chromEnd = self.chromEnd
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	478 strand = 1 if self.strand == '+' else -1
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	479 if frame is not None:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	480 block_sum = sum(self.blockSizes)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	481 offset = (block_sum - frame) % 3
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	482 frame_name = '_' + str(frame + 1)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	483 if self.strand == '+':
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	484 chromStart += frame
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	485 chromEnd -= offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	486 else:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	487 chromStart += offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	488 chromEnd -= frame
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	489 location = "chromosome:%s:%s:%s:%s:%s"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	490 % (reference, self.chrom, chromStart, chromEnd, strand)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	491 seq_id = "%s%s %s %s" % (self.name, frame_name, seqtype, location)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	492 return seq_id
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	493
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	494 def get_line(self, start_offset=0, end_offset=0):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	495 if start_offset or end_offset:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	496 s_offset = start_offset if start_offset else 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	497 e_offset = end_offset if end_offset else 0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	498 if s_offset > self.chromStart:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	499 s_offset = self.chromStart
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	500 chrStart = self.chromStart - s_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	501 chrEnd = self.chromEnd + e_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	502 blkSizes = self.blockSizes
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	503 blkSizes[0] += s_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	504 blkSizes[-1] += e_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	505 blkStarts = self.blockStarts
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	506 for i in range(1, self.blockCount):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	507 blkStarts[i] += s_offset
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	508 items = [str(x) for x in [self.chrom, chrStart, chrEnd, self.name,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	509 self.score, self.strand, self.thickStart,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	510 self.thickEnd, self.itemRgb,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	511 self.blockCount,
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	512 ','.join([str(x) for x in blkSizes]),
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	513 ','.join([str(x) for x in blkStarts])]]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	514 return '\t'.join(items) + '\n'
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0 galaxyp parents: diff changeset	515 return self.line

Mercurial > repos > galaxyp > retrieve_ensembl_bed

annotate bedutil.py @ 2:e385fe93df68 draft default tip