Mercurial > repos > peterjc > blast2go
view tools/ncbi_blast_plus/blast2go.py @ 0:cd52c931b325
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 16:28:31 -0400 |
parents | |
children | 0f159cf346c8 |
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#!/usr/bin/env python """Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.3.5. This script takes exactly three command line arguments: * Input BLAST XML filename * Blast2GO properties filename (settings file) * Output tabular filename It then calls the Java command line tool, and moves the output file to the location Galaxy is expecting. """ import sys import os import subprocess #You may need to edit this to match your local setup, blast2go_jar = "/opt/b2g4pipe/blast2go.jar" def stop_err(msg, error_level=1): """Print error message to stdout and quit with given error level.""" sys.stderr.write("%s\n" % msg) sys.exit(error_level) if len(sys.argv) != 4: stop_err("Require three arguments: XML filename, properties filename, output tabular filename") xml_file, prop_file, tabular_file = sys.argv[1:] if not os.path.isfile(xml_file): stop_err("Input BLAST XML file not found: %s" % xml_file) if not os.path.isfile(prop_file): stop_err("Blast2GO configuration file not found: %s" % prop_file) def run(cmd): #Avoid using shell=True when we call subprocess to ensure if the Python #script is killed, so too is the child process. try: child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except Exception, err: stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) #Use .communicate as can get deadlocks with .wait(), stdout, stderr = child.communicate() return_code = child.returncode if return_code: if stderr and stdout: stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr)) else: stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr)) #For early diagnostics, else: print stdout print stderr if not os.path.isfile(blast2go_jar): stop_err("Blast2GO JAR file not found: %s" % blast2go_jar) #We will have write access whereever the output should be, #so we'll ask Blast2GO to use that as the stem for its output #(it will append .annot to the filename) cmd = ["java", "-jar", blast2go_jar, "-in", xml_file, "-prop", prop_file, "-out", tabular_file, "-a"] run(cmd) out_file = tabular_file + ".annot" if not os.path.isfile(out_file): stop_err("ERROR - No output annotation file from Blast2GO") #Move the output file where Galaxy expects it to be: os.rename(out_file, tabular_file) print "Done"