Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/tmhmm2.py @ 18:eb6ac44d4b8e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Suite v0.2.8, record Promoter 2 verion + misc internal updates
author peterjc
date Tue, 01 Sep 2015 09:56:36 -0400
parents 99b82a2b1272
children f3ecd80850e2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 #ID len ExpAA First60 PredHel Topology
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
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 11
diff changeset
46 from seq_analysis_utils import sys_exit, 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:
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 11
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
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59 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
60 """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
61 count = 0
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 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
63 if not line.strip() or line.startswith("#"):
6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository
peterjc
parents: 1
diff changeset
64 #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
65 continue
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
66 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
67 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
68 identifier, length, expAA, first60, predhel, topology = parts
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
69 except:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
70 assert len(parts)!=6
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 11
diff changeset
71 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
72 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
73 length = length[4:]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74 assert expAA.startswith("ExpAA="), line
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75 expAA = expAA[6:]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
76 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
77 first60 = first60[8:]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
78 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
79 predhel = predhel[8:]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80 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
81 topology = topology[9:]
1
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
82 out_handle.write("%s\t%s\t%s\t%s\t%s\t%s\n" \
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
83 % (identifier, length, expAA, 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
84 count += 1
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
85 return count
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
86
1
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
87 #Note that if the input FASTA file contains no sequences,
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
88 #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
89 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "tmhmm"), FASTA_CHUNK)
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
90 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
91 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
92 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
93
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
94 def clean_up(file_list):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
95 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
96 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
97 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
98 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
99 os.rmdir(tmp_dir)
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
100 except:
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 pass
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
102
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
103 if len(jobs) > 1 and num_threads > 1:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
104 #A small "info" message for Galaxy to show the user.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
105 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
106 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
107 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
108 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
109 if error_level:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
110 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
111 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
112 except IOError:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
113 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
114 clean_up(fasta_files + temp_files)
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 11
diff changeset
115 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
116 error_level)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
117 del results
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
118 del jobs
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
119
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
120 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
121 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
122 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
123 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
124 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
125 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
126 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
127 clean_up(fasta_files + temp_files)
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 11
diff changeset
128 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
129 out_handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
130
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
131 clean_up(fasta_files + temp_files)