tmhmm_and_signalp: tools/protein_analysis/signalp3.py annotate

annotate tools/protein_analysis/signalp3.py @ 29:3cb02adf4326 draft

v0.2.9 Python style improvements

author	peterjc
date	Wed, 01 Feb 2017 09:46:14 -0500
parents	20139cb4c844
children	6d9d7cdf00fc

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
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	55 """
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	56 import sys
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	57 import os
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	58 import tempfile
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	59 from seq_analysis_utils import split_fasta, fasta_iterator
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	60 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	61
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	62 FASTA_CHUNK = 500
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	63 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	64
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	65 if len(sys.argv) not in [6, 8]:
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	66 sys.exit("Require five (or 7) arguments, organism, truncate, threads, "
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	67 "input protein FASTA file & output tabular file (plus "
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	68 "optionally cut method and GFF3 output file). "
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	69 "Got %i arguments." % (len(sys.argv) - 1))
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	70
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	71 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	72 if organism not in ["euk", "gram+", "gram-"]:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	73 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	74
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	75 try:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	76 truncate = int(sys.argv[2])
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	77 except ValueError:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	78 truncate = 0
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	79 if truncate < 0:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	80 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	81
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	82 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	83 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	84 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	85
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	86 if len(sys.argv) == 8:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	87 cut_method = sys.argv[6]
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	88 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	89 sys.exit("Invalid cut method %r" % cut_method)
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	90 gff3_file = sys.argv[7]
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	91 else:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	92 cut_method = None
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	93 gff3_file = None
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	94
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	95
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	96 tmp_dir = tempfile.mkdtemp()
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	97
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	98
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	99 def clean_tabular(raw_handle, out_handle, gff_handle=None, cut_method=None):
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	100 """Clean up SignalP output to make it tabular."""
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	101 if cut_method:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	102 cut_col = {"NN_Cmax": 2,
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	103 "NN_Ymax": 5,
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	104 "NN_Smax": 8,
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	105 "HMM_Cmax": 16}[cut_method]
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	106 else:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	107 cut_col = None
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	108 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	109 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	110 continue
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	111 parts = line.rstrip("\r\n").split()
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	112 assert len(parts) == 21, repr(line)
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	113 assert parts[14].startswith(parts[0]), \
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	114 "Bad entry in SignalP output, ID miss-match:\n%r" % line
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	115 # Remove redundant truncated name column (col 0)
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	116 # 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	117 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	118 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	119
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	120
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	121 def make_gff(fasta_file, tabular_file, gff_file, cut_method):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	122 cut_col, score_col = {"NN_Cmax": (2, 1),
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	123 "NN_Ymax": (5, 4),
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	124 "NN_Smax": (8, 7),
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	125 "HMM_Cmax": (16, 15),
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	126 }[cut_method]
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	127
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	128 source = "SignalP"
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	129 strand = "." # not stranded
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	130 phase = "." # not phased
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	131 tags = "Note=%s" % cut_method
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	132
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	133 tab_handle = open(tabular_file)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	134 line = tab_handle.readline()
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	135 assert line.startswith("#ID\t"), line
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	136
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	137 gff_handle = open(gff_file, "w")
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	138 gff_handle.write("##gff-version 3\n")
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	139
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	140 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	141 parts = line.rstrip("\n").split("\t")
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	142 seqid = parts[0]
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	143 assert title.startswith(seqid), "%s vs %s" % (seqid, title)
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	144 if not seq:
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	145 # 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	146 continue
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	147 cut = int(parts[cut_col])
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	148 if cut == 0:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	149 assert cut_method == "HMM_Cmax", cut_method
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	150 # TODO - Why does it do this?
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	151 cut = 1
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	152 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	153 score = parts[score_col]
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	154 gff_handle.write("##sequence-region %s %i %i\n"
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	155 % (seqid, 1, len(seq)))
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	156 # 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	157 if cut > 1:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	158 # signal_peptide = SO:0000418
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	159 gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n"
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	160 % (seqid, source,
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	161 "signal_peptide", 1, cut - 1,
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	162 score, strand, phase, tags))
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	163 # mature_protein_region = SO:0000419
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	164 gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n"
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	165 % (seqid, source,
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	166 "mature_protein_region", cut, len(seq),
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	167 score, strand, phase, tags))
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	168 tab_handle.close()
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	169 gff_handle.close()
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	170
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	171
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	172 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "signalp"),
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	173 n=FASTA_CHUNK, truncate=truncate, max_len=MAX_LEN)
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	174 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	175 assert len(fasta_files) == len(temp_files)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	176 jobs = ["signalp -short -t %s %s > %s" % (organism, fasta, temp)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	177 for (fasta, temp) in zip(fasta_files, temp_files)]
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	178 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	179
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	180
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	181 def clean_up(file_list):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	182 """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	183 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	184 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	185 os.remove(f)
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	186 try:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	187 os.rmdir(tmp_dir)
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	188 except Exception:
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	189 pass
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	190
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	191 if len(jobs) > 1 and num_threads > 1:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	192 # A small "info" message for Galaxy to show the user.
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	193 print "Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs))
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	194 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	195 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	196 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	197 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	198 try:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	199 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	200 except IOError:
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	201 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	202 if error_level or output.lower().startswith("error running"):
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	203 clean_up(fasta_files + temp_files)
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	204 sys.exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	205 error_level)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	206 del results
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	207
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	208 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	209 fields = ["ID"]
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	210 # NN results:
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	211 for name in ["Cmax", "Ymax", "Smax"]:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	212 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	213 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	214 # HMM results:
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	215 fields.extend(["HMM_type", "HMM_Cmax_score", "HMM_Cmax_pos", "HMM_Cmax_pred",
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	216 "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	217 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	218 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	219 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	220 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	221 data_handle.close()
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	222 out_handle.close()
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	223
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	224 # GFF3:
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	225 if cut_method:
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	226 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	227
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 5 diff changeset	228 clean_up(fasta_files + temp_files)

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/signalp3.py @ 29:3cb02adf4326 draft