tmhmm_and_signalp: tools/protein_analysis/signalp3.py annotate

annotate tools/protein_analysis/signalp3.py @ 19:f3ecd80850e2 draft

v0.2.9 Python style improvements

author	peterjc
date	Wed, 01 Feb 2017 09:46:42 -0500
parents	eb6ac44d4b8e
children	a19b3ded8f33

rev	line source
0 bca9bc7fdaef 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
bca9bc7fdaef 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.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	3
5 0f1c61998b22 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 bca9bc7fdaef 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-)
bca9bc7fdaef 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 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	7 * number of threads to use (integer, defaults to one)
0 bca9bc7fdaef 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	9 * output tabular filename.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	10
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	11 There are two further optional arguments
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	12 * cut type (NN_Cmax, NN_Ymax, NN_Smax or HMM_Cmax)
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	13 * output GFF3 filename
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	14
0 bca9bc7fdaef 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)
bca9bc7fdaef 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	17 for predictions.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	18
bca9bc7fdaef 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
bca9bc7fdaef 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):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	21
bca9bc7fdaef 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
bca9bc7fdaef 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 ?
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 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
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 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
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 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 bca9bc7fdaef 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	28
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef 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:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	32
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	38
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef 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.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	42
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef 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 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	48
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	49 Note that this is somewhat redundant with job-splitting available in Galaxy
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	50 itself (see the SignalP XML file for settings).
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	51
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	52 Finally, you can opt to have a GFF3 file produced which will describe the
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	53 predicted signal peptide and mature peptide for each protein (using one of
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	54 the predictors which gives a cleavage site). WORK IN PROGRESS
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	55 """
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	56 import sys
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	57 import os
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	58 import tempfile
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	59 from seq_analysis_utils import split_fasta, fasta_iterator
9 e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	60 from seq_analysis_utils import run_jobs, thread_count
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	61
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	62 FASTA_CHUNK = 500
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	63 MAX_LEN = 6000 # Found by trial and error
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	64
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	65 if len(sys.argv) not in [6, 8]:
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	66 sys.exit("Require five (or 7) arguments, organism, truncate, threads, "
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	67 "input protein FASTA file & output tabular file (plus "
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	68 "optionally cut method and GFF3 output file). "
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	69 "Got %i arguments." % (len(sys.argv) - 1))
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	70
bca9bc7fdaef 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]
bca9bc7fdaef 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-"]:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	73 sys.exit("Organism argument %s is not one of euk, gram+ or gram-" % organism)
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	74
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	75 try:
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	76 truncate = int(sys.argv[2])
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	77 except ValueError:
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	78 truncate = 0
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	79 if truncate < 0:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	80 sys.exit("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2])
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	81
9 e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	82 num_threads = thread_count(sys.argv[3], default=4)
0 bca9bc7fdaef 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]
bca9bc7fdaef 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]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	85
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	86 if len(sys.argv) == 8:
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	87 cut_method = sys.argv[6]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	88 if cut_method not in ["NN_Cmax", "NN_Ymax", "NN_Smax", "HMM_Cmax"]:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	89 sys.exit("Invalid cut method %r" % cut_method)
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	90 gff3_file = sys.argv[7]
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	91 else:
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	92 cut_method = None
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	93 gff3_file = None
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	94
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	95
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	96 tmp_dir = tempfile.mkdtemp()
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	97
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	98
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	99 def clean_tabular(raw_handle, out_handle, gff_handle=None, cut_method=None):
0 bca9bc7fdaef 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 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	101 if cut_method:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	102 cut_col = {"NN_Cmax": 2,
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	103 "NN_Ymax": 5,
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	104 "NN_Smax": 8,
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	105 "HMM_Cmax": 16}[cut_method]
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	106 else:
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	107 cut_col = None
0 bca9bc7fdaef 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:
bca9bc7fdaef 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("#"):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	110 continue
bca9bc7fdaef 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()
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	112 assert len(parts) == 21, repr(line)
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	113 assert parts[14].startswith(parts[0]), \
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	114 "Bad entry in SignalP output, ID miss-match:\n%r" % line
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	115 # Remove redundant truncated name column (col 0)
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	116 # and put full name at start (col 14)
0 bca9bc7fdaef 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:]
bca9bc7fdaef 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")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	119
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	120
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	121 def make_gff(fasta_file, tabular_file, gff_file, cut_method):
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	122 cut_col, score_col = {"NN_Cmax": (2, 1),
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	123 "NN_Ymax": (5, 4),
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	124 "NN_Smax": (8, 7),
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	125 "HMM_Cmax": (16, 15),
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	126 }[cut_method]
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	127
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	128 source = "SignalP"
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	129 strand = "." # not stranded
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	130 phase = "." # not phased
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	131 tags = "Note=%s" % cut_method
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	132
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	133 tab_handle = open(tabular_file)
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	134 line = tab_handle.readline()
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	135 assert line.startswith("#ID\t"), line
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	136
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	137 gff_handle = open(gff_file, "w")
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	138 gff_handle.write("##gff-version 3\n")
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	139
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	140 for (title, seq), line in zip(fasta_iterator(fasta_file), tab_handle):
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	141 parts = line.rstrip("\n").split("\t")
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	142 seqid = parts[0]
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	143 assert title.startswith(seqid), "%s vs %s" % (seqid, title)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	144 if not seq:
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	145 # Is it possible to have a zero length reference in GFF3?
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	146 continue
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	147 cut = int(parts[cut_col])
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	148 if cut == 0:
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	149 assert cut_method == "HMM_Cmax", cut_method
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	150 # TODO - Why does it do this?
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	151 cut = 1
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	152 assert 1 <= cut <= len(seq), "%i for %s len %i" % (cut, seqid, len(seq))
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	153 score = parts[score_col]
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	154 gff_handle.write("##sequence-region %s %i %i\n"
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	155 % (seqid, 1, len(seq)))
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	156 # If the cut is at the very begining, there is no signal peptide!
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	157 if cut > 1:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	158 # signal_peptide = SO:0000418
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 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 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	160 % (seqid, source,
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	161 "signal_peptide", 1, cut - 1,
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	162 score, strand, phase, tags))
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	163 # mature_protein_region = SO:0000419
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 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 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	165 % (seqid, source,
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	166 "mature_protein_region", cut, len(seq),
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	167 score, strand, phase, tags))
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	168 tab_handle.close()
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	169 gff_handle.close()
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	170
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	171
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	172 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "signalp"),
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	173 n=FASTA_CHUNK, truncate=truncate, max_len=MAX_LEN)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	174 temp_files = [f + ".out" for f in fasta_files]
0 bca9bc7fdaef 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)
bca9bc7fdaef 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)
bca9bc7fdaef 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)]
bca9bc7fdaef 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)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	179
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	180
0 bca9bc7fdaef 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):
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	182 """Remove temp files, and if possible the temp directory."""
0 bca9bc7fdaef 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:
bca9bc7fdaef 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):
bca9bc7fdaef 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 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	186 try:
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	187 os.rmdir(tmp_dir)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	188 except Exception:
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	189 pass
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	190
bca9bc7fdaef 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:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	192 # A small "info" message for Galaxy to show the user.
0 bca9bc7fdaef 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))
bca9bc7fdaef 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)
bca9bc7fdaef 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)
bca9bc7fdaef 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):
bca9bc7fdaef 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]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	198 try:
bca9bc7fdaef 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()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	200 except IOError:
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	201 output = "(no output)"
0 bca9bc7fdaef 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 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	203 clean_up(fasta_files + temp_files)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	204 sys.exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	205 error_level)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	206 del results
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	207
bca9bc7fdaef 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")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	209 fields = ["ID"]
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	210 # NN results:
0 bca9bc7fdaef 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"]:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	212 fields.extend(["NN_%s_score" % name, "NN_%s_pos" % name, "NN_%s_pred" % name])
0 bca9bc7fdaef 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"])
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	214 # HMM results:
0 bca9bc7fdaef 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",
bca9bc7fdaef 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"])
bca9bc7fdaef 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")
bca9bc7fdaef 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:
bca9bc7fdaef 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)
bca9bc7fdaef 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)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	221 data_handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	222 out_handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	223
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	224 # GFF3:
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	225 if cut_method:
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: 9 diff changeset	226 make_gff(fasta_file, tabular_file, gff3_file, cut_method)
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	227
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 5 diff changeset	228 clean_up(fasta_files + temp_files)

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/signalp3.py @ 19:f3ecd80850e2 draft