Mercurial > repos > peterjc > blast2go

annotate tools/ncbi_blast_plus/blast2go.py @ 1:0f159cf346c8

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 16:29:28 -0400
parents cd52c931b325
children a5594772282c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cd52c931b325 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
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
2 """Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.3.5.
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
3
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
4 This script takes exactly three command line arguments:
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
5 * Input BLAST XML filename
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
6 * Blast2GO properties filename (settings file)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
7 * Output tabular filename
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
8
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
9 Sadly b2g4pipe v2.3.5 cannot cope with current style large BLAST XML
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
10 files (e.g. from BLAST 2.2.25+), so we have to reformat these to
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
11 avoid it crashing with a Java heap space OutOfMemoryError.
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
12
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
13 As part of this reformatting, we check for BLASTP or BLASTX output
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
14 (otherwise raise an error), and print the query count.
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
15
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 It then calls the Java command line tool, and moves the output file to
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
17 the location Galaxy is expecting, and removes the tempory XML file.
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18 """
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
19 import sys
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
20 import os
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21 import subprocess
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
22
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
23 #You may need to edit this to match your local setup,
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 blast2go_jar = "/opt/b2g4pipe/blast2go.jar"
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
27 def stop_err(msg, error_level=1):
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
28 """Print error message to stdout and quit with given error level."""
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
29 sys.stderr.write("%s\n" % msg)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30 sys.exit(error_level)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
31
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
32 if len(sys.argv) != 4:
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
33 stop_err("Require three arguments: XML filename, properties filename, output tabular filename")
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
34
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
35 xml_file, prop_file, tabular_file = sys.argv[1:]
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
36
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
37 #We should have write access here:
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
38 tmp_xml_file = tabular_file + ".tmp.xml"
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
39
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
40 if not os.path.isfile(xml_file):
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
41 stop_err("Input BLAST XML file not found: %s" % xml_file)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
42
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
43 if not os.path.isfile(prop_file):
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
44 stop_err("Blast2GO configuration file not found: %s" % prop_file)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
45
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
46 def prepare_xml(original_xml, mangled_xml):
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
47 """Reformat BLAST XML to suit Blast2GO.
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
48
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
49 Blast2GO can't cope with 1000s of <Iteration> tags within a
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
50 single <BlastResult> tag, so instead split this into one
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
51 full XML record per interation (i.e. per query). This gives
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
52 a concatenated XML file mimicing old versions of BLAST.
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
53
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
54 This also checks for BLASTP or BLASTX output, and outputs
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
55 the number of queries. Galaxy will show this as "info".
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
56 """
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
57 in_handle = open(original_xml)
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
58 footer = " </BlastOutput_iterations>\n</BlastOutput>\n"
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
59 header = ""
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
60 while True:
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
61 line = in_handle.readline()
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
62 if not line:
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
63 #No hits?
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
64 stop_err("Problem with XML file?")
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
65 if line.strip() == "<Iteration>":
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
66 break
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
67 header += line
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
68
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
69 if "<BlastOutput_program>blastx</BlastOutput_program>" in header:
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
70 print "BLASTX output identified"
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
71 elif "<BlastOutput_program>blastp</BlastOutput_program>" in header:
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
72 print "BLASTP output identified"
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
73 else:
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
74 in_handle.close()
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
75 stop_err("Expect BLASTP or BLASTX output")
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
76
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
77 out_handle = open(mangled_xml, "w")
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
78 out_handle.write(header)
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
79 out_handle.write(line)
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
80 count = 1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
81 while True:
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
82 line = in_handle.readline()
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
83 if not line:
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
84 break
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
85 elif line.strip() == "<Iteration>":
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
86 #Insert footer/header
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
87 out_handle.write(footer)
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
88 out_handle.write(header)
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
89 count += 1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
90 out_handle.write(line)
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
91
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
92 out_handle.close()
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
93 in_handle.close()
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
94 print "Input has %i queries" % count
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
95
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
96
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
97 def run(cmd):
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
98 #Avoid using shell=True when we call subprocess to ensure if the Python
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
99 #script is killed, so too is the child process.
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
100 try:
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
101 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
102 except Exception, err:
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
103 stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
104 #Use .communicate as can get deadlocks with .wait(),
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
105 stdout, stderr = child.communicate()
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
106 return_code = child.returncode
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
107 if return_code:
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
108 cmd_str = " ".join(cmd)
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
109 if stderr and stdout:
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
110 stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
111 else:
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
112 stop_err("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
113 #For early diagnostics,
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
114 else:
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
115 print stdout
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
116 print stderr
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
117
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
118 if not os.path.isfile(blast2go_jar):
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
119 stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
120
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
121 prepare_xml(xml_file, tmp_xml_file)
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
122 #print "XML file prepared for Blast2GO"
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
123
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
124 #We will have write access wherever the output should be,
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
125 #so we'll ask Blast2GO to use that as the stem for its output
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
126 #(it will append .annot to the filename)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
127 cmd = ["java", "-jar", blast2go_jar,
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
128 "-in", tmp_xml_file,
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
129 "-prop", prop_file,
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
130 "-out", tabular_file, #Used as base name for output files
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
131 "-a", # Generate *.annot tabular file
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
132 #"-img", # Generate images, feature not in v2.3.5
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
133 ]
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
134 #print " ".join(cmd)
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
135 run(cmd)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
136
1
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
137 #Remove the temp XML file
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
138 os.remove(tmp_xml_file)
0f159cf346c8 Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
139
0
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
140 out_file = tabular_file + ".annot"
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
141 if not os.path.isfile(out_file):
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
142 stop_err("ERROR - No output annotation file from Blast2GO")
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
143
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
144 #Move the output file where Galaxy expects it to be:
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
145 os.rename(out_file, tabular_file)
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
146
cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
147 print "Done"