blast_datatypes: blast.py annotate

annotate blast.py @ 19:db2480de852e draft default tip

"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit f726ee4fbfef077d2ffe7e1a67eee254babb7841-dirty"

author	peterjc
date	Fri, 21 Aug 2020 12:39:02 +0000
parents	1250aab8b97a
children

rev	line source
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	1 """NCBI BLAST datatypes.
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	2
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	3 Covers the ``blastxml`` format and the BLAST databases.
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	4 """
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	5
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	6 import logging
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	7 import os
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	8 from time import sleep
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	9
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	10 from galaxy.datatypes.data import Data, Text, get_file_peek
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	11 from galaxy.datatypes.xml import GenericXml
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	12
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	13 log = logging.getLogger(__name__)
5 b3a3ba0c1d47 Uploaded v0.0.15 which updates the BLAST database definitions. peterjc parents: 4 diff changeset	14
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	15 # Note implicit string concatenation here to avoid excessively long lines:
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	16 _DOCTYPES = [
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	17 '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" '
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	18 '"http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	19 '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" '
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	20 '"NCBI_BlastOutput.dtd">',
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	21 ]
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	22
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	23
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	24 class BlastXml(GenericXml):
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	25 """NCBI Blast XML Output data."""
3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	26
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	27 file_ext = "blastxml"
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	28
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	29 def set_peek(self, dataset, is_multi_byte=False):
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	30 """Set the peek and blurb text."""
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	31 if not dataset.dataset.purged:
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	32 dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	33 dataset.blurb = "NCBI Blast XML data"
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	34 else:
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	35 dataset.peek = "file does not exist"
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	36 dataset.blurb = "file purged from disk"
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	37
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	38 def sniff(self, filename):
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	39 """Determine from the contents if the file is blastxml.
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	40
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	41 >>> from galaxy.datatypes.sniff import get_test_fname
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	42 >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml')
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	43 >>> BlastXml().sniff(fname)
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	44 True
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	45 >>> fname = get_test_fname('tblastn_four_human_vs_rhodopsin.xml')
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	46 >>> BlastXml().sniff(fname)
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	47 True
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	48 >>> fname = get_test_fname('interval.interval')
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	49 >>> BlastXml().sniff(fname)
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	50 False
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	51 """
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	52 # TODO - Use a context manager on Python 2.5+ to close handle
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	53 handle = open(filename)
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	54 line = handle.readline()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	55 if line.strip() != '<?xml version="1.0"?>':
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	56 handle.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	57 return False
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	58 line = handle.readline()
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	59 if line.strip() not in _DOCTYPES:
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	60 handle.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	61 return False
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	62 line = handle.readline()
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	63 if line.strip() != "<BlastOutput>":
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	64 handle.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	65 return False
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	66 handle.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	67 return True
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	68
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	69 def merge(split_files, output_file):
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	70 """Merge muliple BLAST XML files into one.
3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	71
3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	72 Merging multiple XML files is non-trivial and must be done in
3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	73 subclasses, rather than the generic parent base XML class.
3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	74 """
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	75 if len(split_files) == 1:
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	76 # For one file only, use base class method (move/copy)
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	77 return Text.merge(split_files, output_file)
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	78 if not split_files:
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	79 raise ValueError(
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	80 "Given no BLAST XML files, %r, to merge into %s"
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	81 % (split_files, output_file)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	82 )
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	83 out = open(output_file, "w")
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	84 h = None
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	85 for f in split_files:
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	86 if not os.path.isfile(f):
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	87 log.warning("BLAST XML file %s missing, retry in 1s..." % f)
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	88 sleep(1)
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	89 if not os.path.isfile(f):
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	90 log.error("BLAST XML file %s missing" % f)
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	91 raise ValueError("BLAST XML file %s missing" % f)
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	92 h = open(f)
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	93 header = h.readline()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	94 if not header:
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	95 out.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	96 h.close()
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	97 # Retry, could be transient error with networked file system...
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	98 log.warning("BLAST XML file %s empty, retry in 1s..." % f)
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	99 sleep(1)
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	100 h = open(f)
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	101 header = h.readline()
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	102 if not header:
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	103 log.error("BLAST XML file %s was empty" % f)
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	104 raise ValueError("BLAST XML file %s was empty" % f)
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	105 if header.strip() != '<?xml version="1.0"?>':
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	106 out.write(header) # for diagnosis
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	107 out.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	108 h.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	109 raise ValueError("%s is not an XML file!" % f)
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	110 line = h.readline()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	111 header += line
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	112 if line.strip() not in _DOCTYPES:
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	113 out.write(header) # for diagnosis
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	114 out.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	115 h.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	116 raise ValueError("%s is not a BLAST XML file!" % f)
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	117 while True:
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	118 line = h.readline()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	119 if not line:
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	120 out.write(header) # for diagnosis
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	121 out.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	122 h.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	123 raise ValueError("BLAST XML file %s ended prematurely" % f)
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	124 header += line
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	125 if "<Iteration>" in line:
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	126 break
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	127 if len(header) > 10000:
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	128 # Something has gone wrong, don't load too much into memory!
623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	129 # Write what we have to the merged file for diagnostics
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	130 out.write(header)
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	131 out.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	132 h.close()
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	133 raise ValueError("The header in BLAST XML file %s is too long" % f)
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	134 if "<BlastOutput>" not in header:
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	135 out.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	136 h.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	137 raise ValueError("%s is not a BLAST XML file:\n%s\n..." % (f, header))
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	138 if f == split_files[0]:
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	139 out.write(header)
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	140 old_header = header
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	141 elif old_header[:300] != header[:300]:
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	142 # Enough to check <BlastOutput_program> and <BlastOutput_version> match
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	143 out.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	144 h.close()
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	145 raise ValueError(
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	146 "BLAST XML headers don't match for %s and %s - have:\n"
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	147 "%s\n...\n\nAnd:\n%s\n...\n"
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	148 % (split_files[0], f, old_header[:300], header[:300])
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	149 )
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	150 else:
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	151 out.write(" <Iteration>\n")
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	152 for line in h:
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	153 if "</BlastOutput_iterations>" in line:
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	154 break
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	155 # TODO - Increment <Iteration_iter-num> and if required automatic query
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	156 # names like <Iteration_query-ID>Query_3</Iteration_query-ID> to be
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	157 # increasing?
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	158 out.write(line)
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	159 h.close()
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	160 out.write(" </BlastOutput_iterations>\n")
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	161 out.write("</BlastOutput>\n")
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	162 out.close()
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	163
3 6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	164 merge = staticmethod(merge)
6ef523b390e0 Uploaded correct file. peterjc parents: diff changeset	165
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	166
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	167 class _BlastDb(object):
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	168 """Base class for BLAST database datatype."""
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	169
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	170 def set_peek(self, dataset, is_multi_byte=False):
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	171 """Set the peek and blurb text."""
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	172 if not dataset.dataset.purged:
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	173 dataset.peek = "BLAST database (multiple files)"
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	174 dataset.blurb = "BLAST database (multiple files)"
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	175 else:
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	176 dataset.peek = "file does not exist"
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	177 dataset.blurb = "file purged from disk"
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	178
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	179 def display_peek(self, dataset):
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	180 """Create HTML content, used for displaying peek."""
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	181 try:
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	182 return dataset.peek
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	183 except Exception:
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	184 return "BLAST database (multiple files)"
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	185
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	186 def display_data(
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	187 self,
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	188 trans,
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	189 data,
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	190 preview=False,
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	191 filename=None,
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	192 to_ext=None,
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	193 size=None,
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	194 offset=None,
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	195 **kwd
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	196 ):
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	197 """Documented as an old display method, but still gets called via tests etc.
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	198
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	199 This allows us to format the data shown in the central pane via the "eye" icon.
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	200 """
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	201 if filename is not None and filename != "index":
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	202 # Change nothing - important for the unit tests to access child files:
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	203 return Data.display_data(
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	204 self, trans, data, preview, filename, to_ext, size, offset, **kwd
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	205 )
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	206 if self.file_ext == "blastdbn":
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	207 title = "This is a nucleotide BLAST database"
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	208 elif self.file_ext == "blastdbp":
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	209 title = "This is a protein BLAST database"
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	210 elif self.file_ext == "blastdbd":
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	211 title = "This is a domain BLAST database"
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	212 else:
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	213 # Error?
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	214 title = "This is a BLAST database."
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	215 msg = ""
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	216 try:
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	217 # Try to use any text recorded in the dummy index file:
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	218 handle = open(data.file_name, "rU")
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	219 msg = handle.read().strip()
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	220 handle.close()
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	221 except Exception:
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	222 pass
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	223 if not msg:
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	224 msg = title
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	225 # Galaxy assumes HTML for the display of composite datatypes,
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	226 return (
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	227 "<html><head><title>%s</title></head><body><pre>%s</pre></body></html>"
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	228 % (title, msg)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	229 )
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	230
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	231 def merge(split_files, output_file):
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	232 """Merge BLAST databases (not implemented for now)."""
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	233 raise NotImplementedError(
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	234 "Merging BLAST databases is non-trivial (do this via makeblastdb?)"
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	235 )
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	236
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	237 def split(cls, input_datasets, subdir_generator_function, split_params):
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	238 """Split a BLAST database (not implemented for now)."""
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	239 if split_params is None:
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	240 return None
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	241 raise NotImplementedError("Can't split BLAST databases")
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	242
f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	243
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	244 class BlastNucDb(_BlastDb, Data):
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	245 """Class for nucleotide BLAST database files."""
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	246
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	247 file_ext = "blastdbn"
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	248 allow_datatype_change = False
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	249 composite_type = "basic"
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	250
5 b3a3ba0c1d47 Uploaded v0.0.15 which updates the BLAST database definitions. peterjc parents: 4 diff changeset	251 def __init__(self, **kwd):
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	252 """Initialize the class."""
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	253 Data.__init__(self, **kwd)
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	254 self.add_composite_file("blastdb.nhr", is_binary=True) # sequence headers
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	255 self.add_composite_file("blastdb.nin", is_binary=True) # index file
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	256 self.add_composite_file("blastdb.nsq", is_binary=True) # nucleotide sequences
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	257
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	258 # alias ( -gi_mask option of makeblastdb)
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	259 self.add_composite_file("blastdb.nal", is_binary=False, optional=True)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	260
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	261 # sorted sequence hash values ( -hash_index option of makeblastdb)
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	262 self.add_composite_file("blastdb.nhd", is_binary=True, optional=True)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	263
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	264 # index of sequence hash values ( -hash_index option of makeblastdb)
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	265 self.add_composite_file("blastdb.nhi", is_binary=True, optional=True)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	266
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	267 # sorted GI values
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	268 # ( -parse_seqids option of makeblastdb and gi present in the description lines)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	269 self.add_composite_file("blastdb.nnd", is_binary=True, optional=True)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	270
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	271 # index of GI values
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	272 # ( -parse_seqids option of makeblastdb and gi present in the description lines)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	273 self.add_composite_file("blastdb.nni", is_binary=True, optional=True)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	274
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	275 # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	276 self.add_composite_file("blastdb.nog", is_binary=True, optional=True)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	277
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	278 # sorted sequence accession values
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	279 # ( -hash_index or -parse_seqids option of makeblastdb)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	280 self.add_composite_file("blastdb.nsd", is_binary=True, optional=True)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	281
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	282 # index of sequence accession values
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	283 # ( -hash_index or -parse_seqids option of makeblastdb)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	284 self.add_composite_file("blastdb.nsi", is_binary=True, optional=True)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	285
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	286 # first volume of the MegaBLAST index generated by makembindex
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	287 # self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True)
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	288 # The previous line should be repeated for each index volume, with filename
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	289 # extensions like '.01.idx', '.02.idx', etc.
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	290
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	291 # MegaBLAST index superheader (-old_style_index false option of makembindex)
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	292 # self.add_composite_file('blastdb.shd', is_binary=True, optional=True)
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	293
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	294 # index of a WriteDB column for e.g. mask data
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	295 # self.add_composite_file('blastdb.naa', is_binary=True, optional=True)
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	296
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	297 # data of a WriteDB column
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	298 # self.add_composite_file('blastdb.nab', is_binary=True, optional=True)
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	299
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	300 # multiple byte order for a WriteDB column
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	301 # self.add_composite_file('blastdb.nac', is_binary=True, optional=True)
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	302
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	303 # The previous 3 lines should be repeated for each WriteDB column, with filename
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	304 # extensions like ('.nba', '.nbb', '.nbc'), ('.nca', '.ncb', '.ncc'), etc.
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	305
5 b3a3ba0c1d47 Uploaded v0.0.15 which updates the BLAST database definitions. peterjc parents: 4 diff changeset	306
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	307 class BlastProtDb(_BlastDb, Data):
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	308 """Class for protein BLAST database files."""
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	309
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	310 file_ext = "blastdbp"
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 7 diff changeset	311 allow_datatype_change = False
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	312 composite_type = "basic"
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	313
5 b3a3ba0c1d47 Uploaded v0.0.15 which updates the BLAST database definitions. peterjc parents: 4 diff changeset	314 def __init__(self, **kwd):
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	315 """Initialize the class."""
4 f9a7783ed7b6 Uploaded v0.0.14 adding BLAST database support. peterjc parents: 3 diff changeset	316 Data.__init__(self, **kwd)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	317 # Component file comments are as in BlastNucDb except where noted
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	318 self.add_composite_file("blastdb.phr", is_binary=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	319 self.add_composite_file("blastdb.pin", is_binary=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	320 self.add_composite_file("blastdb.psq", is_binary=True) # protein sequences
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	321 self.add_composite_file("blastdb.phd", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	322 self.add_composite_file("blastdb.phi", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	323 self.add_composite_file("blastdb.pnd", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	324 self.add_composite_file("blastdb.pni", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	325 self.add_composite_file("blastdb.pog", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	326 self.add_composite_file("blastdb.psd", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	327 self.add_composite_file("blastdb.psi", is_binary=True, optional=True)
15 310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	328 # self.add_composite_file('blastdb.paa', is_binary=True, optional=True)
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	329 # self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	330 # self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	331 # The last 3 lines should be repeated for each WriteDB column, with filename
310ec0f47485 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty peterjc parents: 14 diff changeset	332 # extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc.
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	333
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	334
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 12 diff changeset	335 class BlastDomainDb(_BlastDb, Data):
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	336 """Class for domain BLAST database files."""
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	337
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	338 file_ext = "blastdbd"
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	339 allow_datatype_change = False
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	340 composite_type = "basic"
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	341
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	342 def __init__(self, **kwd):
17 3eada762af11 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty peterjc parents: 15 diff changeset	343 """Initialize the class."""
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	344 Data.__init__(self, **kwd)
18 1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	345 self.add_composite_file("blastdb.phr", is_binary=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	346 self.add_composite_file("blastdb.pin", is_binary=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	347 self.add_composite_file("blastdb.psq", is_binary=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	348 self.add_composite_file("blastdb.freq", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	349 self.add_composite_file("blastdb.loo", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	350 self.add_composite_file("blastdb.psd", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	351 self.add_composite_file("blastdb.psi", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	352 self.add_composite_file("blastdb.rps", is_binary=True, optional=True)
1250aab8b97a planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty peterjc parents: 17 diff changeset	353 self.add_composite_file("blastdb.aux", is_binary=True, optional=True)

Mercurial > repos > devteam > blast_datatypes

annotate blast.py @ 19:db2480de852e draft default tip