Mercurial > repos > peterjc > blast2go

annotate tools/ncbi_blast_plus/blast2go.py @ 0:4bfd64cf18ab

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Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 15:51:25 -0400
parents
children 7b53cc52e7ed
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4bfd64cf18ab Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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1 #!/usr/bin/env python
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2 """Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.3.5.
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3
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4 This script takes exactly three command line arguments:
4bfd64cf18ab Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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5 * Input BLAST XML filename
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6 * Blast2GO properties filename (settings file)
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7 * Output tabular filename
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8
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9 It then calls the Java command line tool, and moves the output file to
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10 the location Galaxy is expecting.
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11 """
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12 import sys
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13 import os
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14 import subprocess
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15
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16 #You may need to edit this to match your local setup,
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17 blast2go_jar = "/opt/b2g4pipe/blast2go.jar"
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18
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19
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20 def stop_err(msg, error_level=1):
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21 """Print error message to stdout and quit with given error level."""
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22 sys.stderr.write("%s\n" % msg)
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23 sys.exit(error_level)
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24
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25 if len(sys.argv) != 4:
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26 stop_err("Require three arguments: XML filename, properties filename, output tabular filename")
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27
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28 xml_file, prop_file, tabular_file = sys.argv[1:]
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29
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30 if not os.path.isfile(xml_file):
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31 stop_err("Input BLAST XML file not found: %s" % xml_file)
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32
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33 if not os.path.isfile(prop_file):
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34 stop_err("Blast2GO configuration file not found: %s" % prop_file)
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35
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36 def run(cmd):
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37 #Avoid using shell=True when we call subprocess to ensure if the Python
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38 #script is killed, so too is the child process.
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39 try:
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40 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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41 except Exception, err:
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42 stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
4bfd64cf18ab Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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43 #Use .communicate as can get deadlocks with .wait(),
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44 stdout, stderr = child.communicate()
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45 return_code = child.returncode
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46 if return_code:
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47 if stderr and stdout:
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48 stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr))
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49 else:
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50 stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr))
4bfd64cf18ab Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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51 #For early diagnostics,
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52 else:
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53 print stdout
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54 print stderr
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55
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56 if not os.path.isfile(blast2go_jar):
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57 stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)
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58
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59 #We will have write access whereever the output should be,
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60 #so we'll ask Blast2GO to use that as the stem for its output
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61 #(it will append .annot to the filename)
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62 cmd = ["java", "-jar", blast2go_jar,
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63 "-in", xml_file,
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64 "-prop", prop_file,
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65 "-out", tabular_file,
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66 "-a"]
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67 run(cmd)
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68
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69 out_file = tabular_file + ".annot"
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70 if not os.path.isfile(out_file):
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71 stop_err("ERROR - No output annotation file from Blast2GO")
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72
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73 #Move the output file where Galaxy expects it to be:
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74 os.rename(out_file, tabular_file)
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75
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76 print "Done"