tmhmm_and_signalp: tools/protein_analysis/tmhmm2.py annotate

annotate tools/protein_analysis/tmhmm2.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 TMHMM v2.0 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
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: 2 diff changeset	4 This script takes exactly three command line arguments - number of threads,
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: 2 diff changeset	5 an input protein FASTA filename, and an output tabular filename. It then
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: 2 diff changeset	6 calls the standalone TMHMM v2.0 program (not the webservice) requesting
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: 2 diff changeset	7 the short output (one line per protein).
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	8
2 6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository peterjc parents: 1 diff changeset	9 The first major feature is cleaning up the tabular output. The short form raw
6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository peterjc parents: 1 diff changeset	10 output from TMHMM v2.0 looks like this (six columns tab separated):
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	11
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	12 gi\|2781234\|pdb\|1JLY\|B len=304 ExpAA=0.01 First60=0.00 PredHel=0 Topology=o
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	13 gi\|4959044\|gb\|AAD34209.1\|AF069992_1 len=600 ExpAA=0.00 First60=0.00 PredHel=0 Topology=o
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	14 gi\|671626\|emb\|CAA85685.1\| len=473 ExpAA=0.19 First60=0.00 PredHel=0 Topology=o
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	15 gi\|3298468\|dbj\|BAA31520.1\| len=107 ExpAA=59.37 First60=31.17 PredHel=3 Topology=o23-45i52-74o89-106i
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	16
2 6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository peterjc parents: 1 diff changeset	17 If there are any additional 'comment' lines starting with the hash (#)
6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository peterjc parents: 1 diff changeset	18 character these are ignored by this script.
6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository peterjc parents: 1 diff changeset	19
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	20 In order to make it easier to use in Galaxy, this wrapper script simplifies
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	21 this to remove the redundant tags, and instead adds a comment line at the
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	22 top with the column names:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	23
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	24 #ID len ExpAA First60 PredHel Topology
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	25 gi\|2781234\|pdb\|1JLY\|B 304 0.01 60 0.00 0 o
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	26 gi\|4959044\|gb\|AAD34209.1\|AF069992_1 600 0.00 0 0.00 0 o
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	27 gi\|671626\|emb\|CAA85685.1\| 473 0.19 0.00 0 o
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	28 gi\|3298468\|dbj\|BAA31520.1\| 107 59.37 31.17 3 o23-45i52-74o89-106i
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	29
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	30 The second major potential feature is taking advantage of multiple cores
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	31 (since TMHMM v2.0 itself is single threaded) by dividing the input FASTA file
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	32 into chunks and running multiple copies of TMHMM in parallel. I would normally
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	33 use Python's multiprocessing library in this situation but it requires at
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	34 least Python 2.6 and at the time of writing Galaxy still supports Python 2.4.
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	35
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: 2 diff changeset	36 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: 2 diff changeset	37 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: 2 diff changeset	38
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	39 Also tmhmm2 can fail without returning an error code, for example if run on a
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	40 64 bit machine with only the 32 bit binaries installed. This script will spot
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	41 when there is no output from tmhmm2, and raise an error.
0 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 import sys
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	44 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: 2 diff changeset	45 import tempfile
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	46 from seq_analysis_utils import split_fasta, 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	47
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	48 FASTA_CHUNK = 500
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	49
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	50 if len(sys.argv) != 4:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	51 sys.exit("Require three arguments, number of threads (int), input protein FASTA file & output tabular file")
9 e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	52
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	53 num_threads = thread_count(sys.argv[1], default=4)
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	54 fasta_file = sys.argv[2]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	55 tabular_file = sys.argv[3]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	56
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: 2 diff changeset	57 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: 2 diff changeset	58
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	59
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	60 def clean_tabular(raw_handle, out_handle):
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	61 """Clean up tabular TMHMM output, returns output line count."""
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	62 count = 0
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	63 for line in raw_handle:
2 6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository peterjc parents: 1 diff changeset	64 if not line.strip() or line.startswith("#"):
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	65 # Ignore any blank lines or comment lines
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	66 continue
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	67 parts = line.rstrip("\r\n").split("\t")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	68 try:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	69 identifier, length, exp_aa, first60, predhel, topology = parts
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	70 except ValueError:
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	71 assert len(parts) != 6
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	72 sys.exit("Bad line: %r" % line)
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	73 assert length.startswith("len="), line
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	74 length = length[4:]
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	75 assert exp_aa.startswith("ExpAA="), line
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	76 exp_aa = exp_aa[6:]
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	77 assert first60.startswith("First60="), line
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	78 first60 = first60[8:]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	79 assert predhel.startswith("PredHel="), line
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	80 predhel = predhel[8:]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	81 assert topology.startswith("Topology="), line
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	82 topology = topology[9:]
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	83 out_handle.write("%s\t%s\t%s\t%s\t%s\t%s\n"
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	84 % (identifier, length, exp_aa, first60, predhel, topology))
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	85 count += 1
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	86 return count
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	87
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	88 # Note that if the input FASTA file contains no sequences,
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	89 # split_fasta returns an empty list (i.e. zero temp files).
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: 2 diff changeset	90 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "tmhmm"), FASTA_CHUNK)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	91 temp_files = [f + ".out" for f in fasta_files]
2 6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository peterjc parents: 1 diff changeset	92 jobs = ["tmhmm -short %s > %s" % (fasta, temp)
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	93 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	94
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	95
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	96 def clean_up(file_list):
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	97 """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	98 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	99 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	100 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: 2 diff changeset	101 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: 2 diff changeset	102 os.rmdir(tmp_dir)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	103 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: 2 diff changeset	104 pass
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	105
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	106 if len(jobs) > 1 and num_threads > 1:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	107 # 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	108 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	109 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	110 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	111 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	112 if error_level:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	113 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	114 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	115 except IOError:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	116 output = ""
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: 2 diff changeset	117 clean_up(fasta_files + temp_files)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	118 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	119 error_level)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	120 del results
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	121 del jobs
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	122
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	123 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	124 out_handle.write("#ID\tlen\tExpAA\tFirst60\tPredHel\tTopology\n")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	125 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	126 data_handle = open(temp)
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	127 count = clean_tabular(data_handle, out_handle)
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	128 data_handle.close()
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	129 if not count:
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: 2 diff changeset	130 clean_up(fasta_files + temp_files)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	131 sys.exit("No output from tmhmm2")
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	132 out_handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	133
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: 2 diff changeset	134 clean_up(fasta_files + temp_files)

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/tmhmm2.py @ 19:f3ecd80850e2 draft