Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/signalp3.py @ 18:eb6ac44d4b8e draft

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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
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1 #!/usr/bin/env python
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2 """Wrapper for SignalP v3.0 for use in Galaxy.
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3
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4 This script takes exactly five command line arguments:
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5 * the organism type (euk, gram+ or gram-)
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6 * length to truncate sequences to (integer)
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7 * number of threads to use (integer, defaults to one)
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8 * an input protein FASTA filename
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9 * output tabular filename.
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10
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11 There are two further optional arguments
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12 * cut type (NN_Cmax, NN_Ymax, NN_Smax or HMM_Cmax)
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13 * output GFF3 filename
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14
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15 It then calls the standalone SignalP v3.0 program (not the webservice)
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16 requesting the short output (one line per protein) using both NN and HMM
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17 for predictions.
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18
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19 First major feature is cleaning up the output. The raw output from SignalP
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20 v3.0 looks like this (21 columns space separated):
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22 # SignalP-NN euk predictions # SignalP-HMM euk predictions
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23 # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? # name ! Cmax pos ? Sprob ?
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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
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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
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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
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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
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29 In order to make it easier to use in Galaxy, this wrapper script reformats
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30 this to use tab separators. Also it removes the redundant truncated name
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31 column, and assigns unique column names in the header:
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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
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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
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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
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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
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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
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38
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39 The second major feature is overcoming SignalP's built in limit of 4000
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40 sequences by breaking up the input FASTA file into chunks. This also allows
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41 us to pre-trim the sequences since SignalP only needs their starts.
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42
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43 The third major feature is taking advantage of multiple cores (since SignalP
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44 v3.0 itself is single threaded) by using the individual FASTA input files to
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45 run multiple copies of TMHMM in parallel. I would normally use Python's
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46 multiprocessing library in this situation but it requires at least Python 2.6
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47 and at the time of writing Galaxy still supports Python 2.4.
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49 Note that this is somewhat redundant with job-splitting available in Galaxy
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50 itself (see the SignalP XML file for settings).
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52 Finally, you can opt to have a GFF3 file produced which will describe the
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53 predicted signal peptide and mature peptide for each protein (using one of
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54 the predictors which gives a cleavage site). *WORK IN PROGRESS*
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55 """
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56 import sys
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57 import os
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58 import tempfile
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59 from seq_analysis_utils import sys_exit, split_fasta, fasta_iterator
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60 from seq_analysis_utils import run_jobs, thread_count
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61
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62 FASTA_CHUNK = 500
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63 MAX_LEN = 6000 #Found by trial and error
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64
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65 if len(sys.argv) not in [6,8]:
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66 sys_exit("Require five (or 7) arguments, organism, truncate, threads, "
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67 "input protein FASTA file & output tabular file (plus "
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68 "optionally cut method and GFF3 output file). "
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69 "Got %i arguments." % (len(sys.argv)-1))
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70
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71 organism = sys.argv[1]
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72 if organism not in ["euk", "gram+", "gram-"]:
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73 sys_exit("Organism argument %s is not one of euk, gram+ or gram-" % organism)
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74
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75 try:
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76 truncate = int(sys.argv[2])
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77 except:
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78 truncate = 0
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79 if truncate < 0:
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80 sys_exit("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2])
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81
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82 num_threads = thread_count(sys.argv[3], default=4)
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83 fasta_file = sys.argv[4]
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84 tabular_file = sys.argv[5]
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85
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86 if len(sys.argv) == 8:
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87 cut_method = sys.argv[6]
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88 if cut_method not in ["NN_Cmax", "NN_Ymax", "NN_Smax", "HMM_Cmax"]:
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89 sys_exit("Invalid cut method %r" % cut_method)
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90 gff3_file = sys.argv[7]
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91 else:
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92 cut_method = None
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93 gff3_file = None
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96 tmp_dir = tempfile.mkdtemp()
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98 def clean_tabular(raw_handle, out_handle, gff_handle=None, cut_method=None):
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99 """Clean up SignalP output to make it tabular."""
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100 if cut_method:
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101 cut_col = {"NN_Cmax" : 2,
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102 "NN_Ymax" : 5,
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103 "NN_Smax" : 8,
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104 "HMM_Cmax" : 16}[cut_method]
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105 else:
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106 cut_col = None
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107 for line in raw_handle:
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108 if not line or line.startswith("#"):
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109 continue
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110 parts = line.rstrip("\r\n").split()
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111 assert len(parts)==21, repr(line)
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112 assert parts[14].startswith(parts[0]), \
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113 "Bad entry in SignalP output, ID miss-match:\n%r" % line
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114 #Remove redundant truncated name column (col 0)
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115 #and put full name at start (col 14)
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116 parts = parts[14:15] + parts[1:14] + parts[15:]
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117 out_handle.write("\t".join(parts) + "\n")
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118
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119 def make_gff(fasta_file, tabular_file, gff_file, 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
120 cut_col, score_col = {"NN_Cmax" : (2,1),
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
121 "NN_Ymax" : (5,4),
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peterjc
parents: 5
diff changeset
122 "NN_Smax" : (8,7),
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
123 "HMM_Cmax" : (16,15),
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
124 }[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
125
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 source = "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
127 strand = "." #not stranded
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 phase = "." #not phased
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
129 tags = "Note=%s" % 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
130
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 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
132 line = tab_handle.readline()
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peterjc
parents: 5
diff changeset
133 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
134
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 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
136 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
137
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 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
139 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
140 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
141 assert title.startswith(seqid), "%s vs %s" % (seqid, title)
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 if len(seq)==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 #Is it possible to have a zero length reference in GFF3?
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
144 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
145 cut = int(parts[cut_col])
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peterjc
parents: 5
diff changeset
146 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
147 assert cut_method == "HMM_Cmax", 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
148 #TODO - Why does it do this?
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 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
150 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
151 score = parts[score_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
152 gff_handle.write("##sequence-region %s %i %i\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
153 % (seqid, 1, 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
154 #If the cut is at the very begining, there is no signal peptide!
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 if 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
156 #signal_peptide = SO:0000418
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 gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\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
158 % (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
159 "signal_peptide", 1, 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
160 score, strand, phase, tags))
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
161 #mature_protein_region = SO:0000419
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 gff_handle.write("%s\t%s\t%s\t%i\t%i\t%s\t%s\t%s\t%s\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
163 % (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
164 "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
165 score, strand, phase, tags))
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 tab_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
167 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
168
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
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 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
171 n=FASTA_CHUNK, truncate=truncate, max_len=MAX_LEN)
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
172 temp_files = [f+".out" for f in fasta_files]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
173 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
174 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
175 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
176 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
177
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
178 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
179 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
180 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
181 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
182 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
183 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: 5
diff changeset
184 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: 5
diff changeset
185 pass
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
186
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
187 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
188 #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
189 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
190 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
191 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
192 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
193 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
194 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
195 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
196 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
197 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
198 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
199 clean_up(fasta_files + temp_files)
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 11
diff changeset
200 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
201 error_level)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
202 del results
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
203
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
204 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
205 fields = ["ID"]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
206 #NN results:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
207 for name in ["Cmax", "Ymax", "Smax"]:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
208 fields.extend(["NN_%s_score"%name, "NN_%s_pos"%name, "NN_%s_pred"%name])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
209 fields.extend(["NN_Smean_score", "NN_Smean_pred", "NN_D_score", "NN_D_pred"])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
210 #HMM results:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
211 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
212 "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
213 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
214 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
215 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
216 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
217 data_handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
218 out_handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
219
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
220 #GFF3:
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
221 if cut_method:
11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
peterjc
parents: 9
diff changeset
222 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
223
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
224 clean_up(fasta_files + temp_files)