Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/signalp3.py @ 7:5e62aefb2918 draft
Uploaded v0.1.2 to Test Tool Shed
| author | peterjc |
|---|---|
| date | Tue, 26 Mar 2013 14:24:56 -0400 |
| parents | ef7ceca37e3f |
| children | 391a142c1e60 |
| 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 | 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 | 11 There are two further optional arguments |
| 12 * cut type (NN_Cmax, NN_Ymax, NN_Smax or HMM_Cmax) | |
| 13 * output GFF3 filename | |
| 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 ? |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
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 |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
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 |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
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 |
|
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 | 48 |
| 49 Note that this is somewhat redundant with job-splitting available in Galaxy | |
| 50 itself (see the SignalP XML file for settings). | |
| 51 | |
| 52 Finally, you can opt to have a GFF3 file produced which will describe the | |
| 53 predicted signal peptide and mature peptide for each protein (using one of | |
| 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 | 58 import tempfile |
| 59 from seq_analysis_utils import stop_err, split_fasta, fasta_iterator | |
| 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 |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
63 MAX_LEN = 6000 #Found by trial and error |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
64 |
| 7 | 65 if len(sys.argv) not in [6,8]: |
| 66 stop_err("Require five (or 7) arguments, organism, truncate, threads, " | |
| 67 "input protein FASTA file & output tabular file (plus " | |
| 68 "optionally cut method and GFF3 output file). " | |
| 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-"]: |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
73 stop_err("Organism argument %s is not one of euk, gram+ or gram-" % organism) |
|
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: |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
76 truncate = int(sys.argv[2]) |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
77 except: |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
78 truncate = 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: |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
80 stop_err("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2]) |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
81 |
| 7 | 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 | 86 if len(sys.argv) == 8: |
| 87 cut_method = sys.argv[6] | |
| 88 if cut_method not in ["NN_Cmax", "NN_Ymax", "NN_Smax", "HMM_Cmax"]: | |
| 89 stop_err("Invalid cut method %r" % cut_method) | |
| 90 gff3_file = sys.argv[7] | |
| 91 else: | |
| 92 cut_method = None | |
| 93 gff3_file = None | |
| 94 | |
| 95 | |
| 96 tmp_dir = tempfile.mkdtemp() | |
| 97 | |
| 98 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
|
99 """Clean up SignalP output to make it tabular.""" |
| 7 | 100 if cut_method: |
| 101 cut_col = {"NN_Cmax" : 2, | |
| 102 "NN_Ymax" : 5, | |
| 103 "NN_Smax" : 8, | |
| 104 "HMM_Cmax" : 16}[cut_method] | |
| 105 else: | |
| 106 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
|
107 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
|
108 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
|
109 continue |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
110 parts = line.rstrip("\r\n").split() |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
111 assert len(parts)==21, repr(line) |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
112 assert parts[14].startswith(parts[0]) |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
113 #Remove redundant truncated name column (col 0) |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
114 #and put full name at start (col 14) |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
115 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
|
116 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
|
117 |
| 7 | 118 def make_gff(fasta_file, tabular_file, gff_file, cut_method): |
| 119 cut_col, score_col = {"NN_Cmax" : (2,1), | |
| 120 "NN_Ymax" : (5,4), | |
| 121 "NN_Smax" : (8,7), | |
| 122 "HMM_Cmax" : (16,15), | |
| 123 }[cut_method] | |
| 124 | |
| 125 source = "SignalP" | |
| 126 strand = "." #not stranded | |
| 127 phase = "." #not phased | |
| 128 tags = "Note=%s" % cut_method | |
| 129 | |
| 130 tab_handle = open(tabular_file) | |
| 131 line = tab_handle.readline() | |
| 132 assert line.startswith("#ID\t"), line | |
| 133 | |
| 134 gff_handle = open(gff_file, "w") | |
| 135 gff_handle.write("##gff-version 3\n") | |
| 136 | |
| 137 for (title, seq), line in zip(fasta_iterator(fasta_file), tab_handle): | |
| 138 parts = line.rstrip("\n").split("\t") | |
| 139 seqid = parts[0] | |
| 140 assert title.startswith(seqid), "%s vs %s" % (seqid, title) | |
| 141 if len(seq)==0: | |
| 142 #Is it possible to have a zero length reference in GFF3? | |
| 143 continue | |
| 144 cut = int(parts[cut_col]) | |
| 145 if cut == 0: | |
| 146 assert cut_method == "HMM_Cmax", cut_method | |
| 147 #TODO - Why does it do this? | |
| 148 cut = 1 | |
| 149 assert 1 <= cut <= len(seq), "%i for %s len %i" % (cut, seqid, len(seq)) | |
| 150 score = parts[score_col] | |
| 151 gff_handle.write("##sequence-region %s %i %i\n" \ | |
| 152 % (seqid, 1, len(seq))) | |
| 153 #If the cut is at the very begining, there is no signal peptide! | |
| 154 if cut > 1: | |
| 155 #signal_peptide = SO:0000418 | |
| 156 gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n" \ | |
| 157 % (seqid, source, | |
| 158 "signal_peptide", 1, cut-1, | |
| 159 score, strand, phase, tags)) | |
| 160 #mature_protein_region = SO:0000419 | |
| 161 gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\n" \ | |
| 162 % (seqid, source, | |
| 163 "mature_protein_region", cut, len(seq), | |
| 164 score, strand, phase, tags)) | |
| 165 tab_handle.close() | |
| 166 gff_handle.close() | |
| 167 | |
| 168 | |
| 169 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "signalp"), | |
| 170 n=FASTA_CHUNK, truncate=truncate, max_len=MAX_LEN) | |
|
0
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
171 temp_files = [f+".out" for f in fasta_files] |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
172 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
|
173 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
|
174 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
|
175 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
|
176 |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
177 def clean_up(file_list): |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
178 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
|
179 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
|
180 os.remove(f) |
| 7 | 181 try: |
| 182 os.rmdir(tmp_dir) | |
| 183 except: | |
| 184 pass | |
|
0
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
185 |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
186 if len(jobs) > 1 and num_threads > 1: |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
187 #A small "info" message for Galaxy to show the user. |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
188 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
|
189 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
|
190 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
|
191 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
|
192 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
|
193 try: |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
194 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
|
195 except IOError: |
| 7 | 196 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
|
197 if error_level or output.lower().startswith("error running"): |
| 7 | 198 clean_up(fasta_files + temp_files) |
|
0
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
199 stop_err("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output), |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
200 error_level) |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
201 del results |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
202 |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
203 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
|
204 fields = ["ID"] |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
205 #NN results: |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
206 for name in ["Cmax", "Ymax", "Smax"]: |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
207 fields.extend(["NN_%s_score"%name, "NN_%s_pos"%name, "NN_%s_pred"%name]) |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
208 fields.extend(["NN_Smean_score", "NN_Smean_pred", "NN_D_score", "NN_D_pred"]) |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
209 #HMM results: |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
210 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
|
211 "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
|
212 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
|
213 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
|
214 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
|
215 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
|
216 data_handle.close() |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
217 out_handle.close() |
|
a2eeeaa6f75e
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
218 |
| 7 | 219 #GFF3: |
| 220 if cut_method: | |
| 221 make_gff(fasta_file, tabular_file, gff3_file, cut_method) | |
| 222 | |
| 223 clean_up(fasta_files + temp_files) |