tmhmm_and_signalp: tools/protein_analysis/signalp3.py annotate

annotate tools/protein_analysis/signalp3.py @ 34:7a2e20baacee draft default tip

"v0.2.13 - Python 3 fix for raising StopIteration"

author	peterjc
date	Thu, 17 Jun 2021 17:58:23 +0000
parents	20da7f48b56f
children

rev	line source
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	1 #!/usr/bin/env python
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	2 """Wrapper for SignalP v3.0 for use in Galaxy.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	3
5 ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	4 This script takes exactly five command line arguments:
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	5 * the organism type (euk, gram+ or gram-)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	6 * length to truncate sequences to (integer)
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	7 * number of threads to use (integer, defaults to one)
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	8 * an input protein FASTA filename
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	9 * output tabular filename.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	10
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	11 There are two further optional arguments
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	12 * cut type (NN_Cmax, NN_Ymax, NN_Smax or HMM_Cmax)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	13 * output GFF3 filename
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	14
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	15 It then calls the standalone SignalP v3.0 program (not the webservice)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	16 requesting the short output (one line per protein) using both NN and HMM
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	17 for predictions.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	18
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	19 First major feature is cleaning up the output. The raw output from SignalP
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	20 v3.0 looks like this (21 columns space separated):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	21
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	22 # SignalP-NN euk predictions # SignalP-HMM euk predictions
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	23 # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? # name ! Cmax pos ? Sprob ?
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	24 gi\|2781234\|pdb\|1JLY\| 0.061 17 N 0.043 17 N 0.199 1 N 0.067 N 0.055 N gi\|2781234\|pdb\|1JLY\|B Q 0.000 17 N 0.000 N
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	25 gi\|4959044\|gb\|AAD342 0.099 191 N 0.012 38 N 0.023 12 N 0.014 N 0.013 N gi\|4959044\|gb\|AAD34209.1\|AF069992_1 Q 0.000 0 N 0.000 N
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	26 gi\|671626\|emb\|CAA856 0.139 381 N 0.020 8 N 0.121 4 N 0.067 N 0.044 N gi\|671626\|emb\|CAA85685.1\| Q 0.000 0 N 0.000 N
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	27 gi\|3298468\|dbj\|BAA31 0.208 24 N 0.184 38 N 0.980 32 Y 0.613 Y 0.398 N gi\|3298468\|dbj\|BAA31520.1\| Q 0.066 24 N 0.139 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	28
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	29 In order to make it easier to use in Galaxy, this wrapper script reformats
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	30 this to use tab separators. Also it removes the redundant truncated name
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	31 column, and assigns unique column names in the header:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	32
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	33 #ID NN_Cmax_score NN_Cmax_pos NN_Cmax_pred NN_Ymax_score NN_Ymax_pos NN_Ymax_pred NN_Smax_score NN_Smax_pos NN_Smax_pred NN_Smean_score NN_Smean_pred NN_D_score NN_D_pred HMM_bang HMM_Cmax_score HMM_Cmax_pos HMM_Cmax_pred HMM_Sprob_score HMM_Sprob_pred
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	34 gi\|2781234\|pdb\|1JLY\|B 0.061 17 N 0.043 17 N 0.199 1 N 0.067 N 0.055 N Q 0.000 17 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	35 gi\|4959044\|gb\|AAD34209.1\|AF069992_1 0.099 191 N 0.012 38 N 0.023 12 N 0.014 N 0.013 N Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	36 gi\|671626\|emb\|CAA85685.1\| 0.139 381 N 0.020 8 N 0.121 4 N 0.067 N 0.044 N Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	37 gi\|3298468\|dbj\|BAA31520.1\| 0.208 24 N 0.184 38 N 0.980 32 Y 0.613 Y 0.398 N Q 0.066 24 N 0.139 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	38
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	39 The second major feature is overcoming SignalP's built in limit of 4000
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	40 sequences by breaking up the input FASTA file into chunks. This also allows
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	41 us to pre-trim the sequences since SignalP only needs their starts.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	42
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	43 The third major feature is taking advantage of multiple cores (since SignalP
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	44 v3.0 itself is single threaded) by using the individual FASTA input files to
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	45 run multiple copies of TMHMM in parallel. I would normally use Python's
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	46 multiprocessing library in this situation but it requires at least Python 2.6
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	47 and at the time of writing Galaxy still supports Python 2.4.
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	48
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	49 Note that this is somewhat redundant with job-splitting available in Galaxy
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	50 itself (see the SignalP XML file for settings).
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	51
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	52 Finally, you can opt to have a GFF3 file produced which will describe the
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	53 predicted signal peptide and mature peptide for each protein (using one of
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	54 the predictors which gives a cleavage site). WORK IN PROGRESS
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	55 """ # noqa: E501
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	56
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	57 from __future__ import print_function
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	58
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	59 import os
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	60 import sys
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	61 import tempfile
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	62
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	63 from seq_analysis_utils import fasta_iterator, split_fasta
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	64 from seq_analysis_utils import run_jobs, thread_count
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	65
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	66 FASTA_CHUNK = 500
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	67 MAX_LEN = 6000 # Found by trial and error
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	68
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	69 if "-v" in sys.argv or "--version" in sys.argv:
34 7a2e20baacee "v0.2.13 - Python 3 fix for raising StopIteration" peterjc parents: 32 diff changeset	70 print("SignalP Galaxy wrapper version 0.0.20")
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	71 sys.exit(os.system("signalp -version"))
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	72
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	73 if len(sys.argv) not in [6, 8]:
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	74 sys.exit(
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	75 "Require five (or 7) arguments, organism, truncate, threads, "
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	76 "input protein FASTA file & output tabular file (plus "
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	77 "optionally cut method and GFF3 output file). "
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	78 "Got %i arguments." % (len(sys.argv) - 1)
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	79 )
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	80
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	81 organism = sys.argv[1]
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	82 if organism not in ["euk", "gram+", "gram-"]:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	83 sys.exit("Organism argument %s is not one of euk, gram+ or gram-" % organism)
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	84
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	85 try:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	86 truncate = int(sys.argv[2])
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	87 except ValueError:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	88 truncate = 0
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	89 if truncate < 0:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	90 sys.exit("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2])
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	91
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	92 num_threads = thread_count(sys.argv[3], default=4)
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	93 fasta_file = sys.argv[4]
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	94 tabular_file = sys.argv[5]
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	95
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	96 if len(sys.argv) == 8:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	97 cut_method = sys.argv[6]
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	98 if cut_method not in ["NN_Cmax", "NN_Ymax", "NN_Smax", "HMM_Cmax"]:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	99 sys.exit("Invalid cut method %r" % cut_method)
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	100 gff3_file = sys.argv[7]
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	101 else:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	102 cut_method = None
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	103 gff3_file = None
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	104
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	105
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	106 tmp_dir = tempfile.mkdtemp()
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	107
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	108
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	109 def clean_tabular(raw_handle, out_handle, gff_handle=None):
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	110 """Clean up SignalP output to make it tabular."""
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	111 for line in raw_handle:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	112 if not line or line.startswith("#"):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	113 continue
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	114 parts = line.rstrip("\r\n").split()
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	115 assert len(parts) == 21, repr(line)
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	116 assert parts[14].startswith(parts[0]), (
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	117 "Bad entry in SignalP output, ID miss-match:\n%r" % line
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	118 )
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	119 # Remove redundant truncated name column (col 0)
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	120 # and put full name at start (col 14)
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	121 parts = parts[14:15] + parts[1:14] + parts[15:]
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	122 out_handle.write("\t".join(parts) + "\n")
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	123
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	124
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	125 def make_gff(fasta_file, tabular_file, gff_file, cut_method):
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	126 """Make a GFF file."""
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	127 cut_col, score_col = {
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	128 "NN_Cmax": (2, 1),
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	129 "NN_Ymax": (5, 4),
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	130 "NN_Smax": (8, 7),
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	131 "HMM_Cmax": (16, 15),
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	132 }[cut_method]
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	133
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	134 source = "SignalP"
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	135 strand = "." # not stranded
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	136 phase = "." # not phased
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	137 tags = "Note=%s" % cut_method
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	138
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	139 tab_handle = open(tabular_file)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	140 line = tab_handle.readline()
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	141 assert line.startswith("#ID\t"), line
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	142
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	143 gff_handle = open(gff_file, "w")
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	144 gff_handle.write("##gff-version 3\n")
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	145
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	146 for (title, seq), line in zip(fasta_iterator(fasta_file), tab_handle):
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	147 parts = line.rstrip("\n").split("\t")
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	148 seqid = parts[0]
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	149 assert title.startswith(seqid), "%s vs %s" % (seqid, title)
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	150 if not seq:
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	151 # Is it possible to have a zero length reference in GFF3?
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	152 continue
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	153 cut = int(parts[cut_col])
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	154 if cut == 0:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	155 assert cut_method == "HMM_Cmax", cut_method
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	156 # TODO - Why does it do this?
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	157 cut = 1
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	158 assert 1 <= cut <= len(seq), "%i for %s len %i" % (cut, seqid, len(seq))
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	159 score = parts[score_col]
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	160 gff_handle.write("##sequence-region %s %i %i\n" % (seqid, 1, len(seq)))
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	161 # If the cut is at the very begining, there is no signal peptide!
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	162 if cut > 1:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	163 # signal_peptide = SO:0000418
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	164 gff_handle.write(
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	165 "%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n"
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	166 % (
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	167 seqid,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	168 source,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	169 "signal_peptide",
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	170 1,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	171 cut - 1,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	172 score,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	173 strand,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	174 phase,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	175 tags,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	176 )
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	177 )
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	178 # mature_protein_region = SO:0000419
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	179 gff_handle.write(
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	180 "%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n"
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	181 % (
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	182 seqid,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	183 source,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	184 "mature_protein_region",
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	185 cut,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	186 len(seq),
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	187 score,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	188 strand,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	189 phase,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	190 tags,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	191 )
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	192 )
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	193 tab_handle.close()
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	194 gff_handle.close()
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	195
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	196
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	197 if num_threads == 1:
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	198 # Still want to call split_fasta to apply truncation, but
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	199 # no reason to make multiple files - and more chance of
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	200 # hitting file system glitches if we do. So,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	201 FASTA_CHUNK = sys.maxsize
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	202
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	203 fasta_files = split_fasta(
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	204 fasta_file,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	205 os.path.join(tmp_dir, "signalp"),
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	206 n=FASTA_CHUNK,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	207 truncate=truncate,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	208 max_len=MAX_LEN,
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	209 )
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	210 temp_files = [f + ".out" for f in fasta_files]
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	211 assert len(fasta_files) == len(temp_files)
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	212 jobs = [
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	213 "signalp -short -t %s %s > %s" % (organism, fasta, temp)
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	214 for (fasta, temp) in zip(fasta_files, temp_files)
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	215 ]
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	216 assert len(fasta_files) == len(temp_files) == len(jobs)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	217
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	218
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	219 def clean_up(file_list):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	220 """Remove temp files, and if possible the temp directory."""
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	221 for f in file_list:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	222 if os.path.isfile(f):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	223 os.remove(f)
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	224 try:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	225 os.rmdir(tmp_dir)
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	226 except Exception:
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	227 pass
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	228
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	229
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	230 if len(jobs) > 1 and num_threads > 1:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	231 # A small "info" message for Galaxy to show the user.
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	232 print("Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs)))
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	233 results = run_jobs(jobs, num_threads)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	234 assert len(fasta_files) == len(temp_files) == len(jobs)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	235 for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	236 error_level = results[cmd]
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	237 try:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	238 output = open(temp).readline()
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	239 except IOError:
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	240 output = "(no output)"
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	241 if error_level or output.lower().startswith("error running"):
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	242 clean_up(fasta_files + temp_files)
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	243 if output:
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	244 sys.stderr.write(
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	245 "One or more tasks failed, e.g. %i from %r gave:\n%s"
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	246 % (error_level, cmd, output)
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	247 )
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	248 else:
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	249 sys.stderr.write(
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	250 "One or more tasks failed, e.g. %i from %r with no output\n"
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	251 % (error_level, cmd)
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	252 )
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 29 diff changeset	253 sys.exit(error_level)
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	254 del results
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	255
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	256 out_handle = open(tabular_file, "w")
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	257 fields = ["ID"]
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	258 # NN results:
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	259 for name in ["Cmax", "Ymax", "Smax"]:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	260 fields.extend(["NN_%s_score" % name, "NN_%s_pos" % name, "NN_%s_pred" % name])
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	261 fields.extend(["NN_Smean_score", "NN_Smean_pred", "NN_D_score", "NN_D_pred"])
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	262 # HMM results:
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	263 fields.extend(
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	264 [
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	265 "HMM_type",
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	266 "HMM_Cmax_score",
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	267 "HMM_Cmax_pos",
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	268 "HMM_Cmax_pred",
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	269 "HMM_Sprob_score",
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	270 "HMM_Sprob_pred",
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	271 ]
20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	272 )
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	273 out_handle.write("#" + "\t".join(fields) + "\n")
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	274 for temp in temp_files:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	275 data_handle = open(temp)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	276 clean_tabular(data_handle, out_handle)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	277 data_handle.close()
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	278 out_handle.close()
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	279
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	280 # GFF3:
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	281 if cut_method:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	282 make_gff(fasta_file, tabular_file, gff3_file, cut_method)
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	283
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	284 clean_up(fasta_files + temp_files)

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/signalp3.py @ 34:7a2e20baacee draft default tip