Mercurial > repos > peterjc > blast2go

annotate tools/blast2go/blast2go.py @ 5:e4419efbefad draft

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Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
author peterjc
date Fri, 22 Feb 2013 08:47:27 -0500
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5
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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1 #!/usr/bin/env python
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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2 """Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.5.
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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3
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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4 This script takes exactly three command line arguments:
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5 * Input BLAST XML filename
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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6 * Blast2GO properties filename (settings file)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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7 * Output tabular filename
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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8
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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9 The properties filename can be a fully qualified path, but if not
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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10 this will look next to the blast2go.jar file.
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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11
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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12 Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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13 style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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14 these to avoid it crashing with a Java heap space OutOfMemoryError.
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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15
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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16 As part of this reformatting, we check for BLASTP or BLASTX output
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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17 (otherwise raise an error), and print the query count.
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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18
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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19 It then calls the Java command line tool, and moves the output file to
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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20 the location Galaxy is expecting, and removes the tempory XML file.
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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21 """
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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22 import sys
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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23 import os
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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24 import subprocess
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25
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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26 #You may need to edit this to match your local setup,
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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27 #blast2go_jar = "/opt/b2g4pipe/blast2go.jar"
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28 blast2go_jar = "/opt/b2g4pipe_v2.5/blast2go.jar"
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29
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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30
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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31 def stop_err(msg, error_level=1):
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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32 """Print error message to stdout and quit with given error level."""
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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33 sys.stderr.write("%s\n" % msg)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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34 sys.exit(error_level)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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35
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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36 if len(sys.argv) != 4:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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37 stop_err("Require three arguments: XML filename, properties filename, output tabular filename")
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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38
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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39 xml_file, prop_file, tabular_file = sys.argv[1:]
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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40
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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41 #We should have write access here:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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42 tmp_xml_file = tabular_file + ".tmp.xml"
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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43
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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44 if not os.path.isfile(blast2go_jar):
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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45 stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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46
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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47 if not os.path.isfile(xml_file):
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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48 stop_err("Input BLAST XML file not found: %s" % xml_file)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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49
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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50 if not os.path.isfile(prop_file):
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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51 tmp = os.path.join(os.path.split(blast2go_jar)[0], prop_file)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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52 if os.path.isfile(tmp):
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
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53 #The properties file seems to have been given relative to the JAR
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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54 prop_file = tmp
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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55 else:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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56 stop_err("Blast2GO configuration file not found: %s" % prop_file)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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57 del tmp
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58
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59 def prepare_xml(original_xml, mangled_xml):
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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60 """Reformat BLAST XML to suit Blast2GO.
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61
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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62 Blast2GO can't cope with 1000s of <Iteration> tags within a
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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63 single <BlastResult> tag, so instead split this into one
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64 full XML record per interation (i.e. per query). This gives
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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65 a concatenated XML file mimicing old versions of BLAST.
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66
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67 This also checks for BLASTP or BLASTX output, and outputs
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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68 the number of queries. Galaxy will show this as "info".
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69 """
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70 in_handle = open(original_xml)
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71 footer = " </BlastOutput_iterations>\n</BlastOutput>\n"
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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72 header = ""
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73 while True:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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74 line = in_handle.readline()
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75 if not line:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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76 #No hits?
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77 stop_err("Problem with XML file?")
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78 if line.strip() == "<Iteration>":
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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79 break
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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80 header += line
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81
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82 if "<BlastOutput_program>blastx</BlastOutput_program>" in header:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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83 print "BLASTX output identified"
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84 elif "<BlastOutput_program>blastp</BlastOutput_program>" in header:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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85 print "BLASTP output identified"
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86 else:
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87 in_handle.close()
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88 stop_err("Expect BLASTP or BLASTX output")
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89
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90 out_handle = open(mangled_xml, "w")
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91 out_handle.write(header)
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92 out_handle.write(line)
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93 count = 1
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94 while True:
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95 line = in_handle.readline()
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96 if not line:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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97 break
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98 elif line.strip() == "<Iteration>":
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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99 #Insert footer/header
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100 out_handle.write(footer)
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101 out_handle.write(header)
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102 count += 1
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103 out_handle.write(line)
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104
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diff changeset
105 out_handle.close()
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106 in_handle.close()
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107 print "Input has %i queries" % count
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108
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109
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110 def run(cmd):
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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111 #Avoid using shell=True when we call subprocess to ensure if the Python
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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112 #script is killed, so too is the child process.
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113 try:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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114 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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115 except Exception, err:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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116 stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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117 #Use .communicate as can get deadlocks with .wait(),
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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118 stdout, stderr = child.communicate()
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119 return_code = child.returncode
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120
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121 #keep stdout minimal as shown prominently in Galaxy
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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122 #Record it in case a silent error needs diagnosis
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123 if stdout:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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124 sys.stderr.write("Standard out:\n%s\n\n" % stdout)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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125 if stderr:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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126 sys.stderr.write("Standard error:\n%s\n\n" % stderr)
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127
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128 error_msg = None
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129 if return_code:
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130 cmd_str = " ".join(cmd)
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131 error_msg = "Return code %i from command:\n%s" % (return_code, cmd_str)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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132 elif "Database or network connection (timeout) error" in stdout+stderr:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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133 error_msg = "Database or network connection (timeout) error"
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diff changeset
134 elif "Annotation of 0 seqs with 0 annots finished." in stdout+stderr:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
135 error_msg = "No sequences processed!"
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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136
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diff changeset
137 if error_msg:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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138 print error_msg
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diff changeset
139 stop_err(error_msg)
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140
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141
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diff changeset
142 blast2go_classpath = os.path.split(blast2go_jar)[0]
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
143 assert os.path.isdir(blast2go_classpath)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
144 blast2go_classpath = "%s/*:%s/ext/*:" % (blast2go_classpath, blast2go_classpath)
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145
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diff changeset
146 prepare_xml(xml_file, tmp_xml_file)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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147 #print "XML file prepared for Blast2GO"
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148
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149 #We will have write access wherever the output should be,
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
150 #so we'll ask Blast2GO to use that as the stem for its output
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
151 #(it will append .annot to the filename)
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diff changeset
152 cmd = ["java", "-cp", blast2go_classpath, "es.blast2go.prog.B2GAnnotPipe",
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
153 "-in", tmp_xml_file,
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
154 "-prop", prop_file,
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
155 "-out", tabular_file, #Used as base name for output files
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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156 "-annot", # Generate *.annot tabular file
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diff changeset
157 #NOTE: For v2.3.5 must use -a, for v2.5 must use -annot instead
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
158 #"-img", # Generate images, feature not in v2.3.5
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
159 ]
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diff changeset
160 #print " ".join(cmd)
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parents:
diff changeset
161 run(cmd)
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162
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diff changeset
163 #Remove the temp XML file
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diff changeset
164 os.remove(tmp_xml_file)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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diff changeset
165
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parents:
diff changeset
166 out_file = tabular_file + ".annot"
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
parents:
diff changeset
167 if not os.path.isfile(out_file):
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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parents:
diff changeset
168 stop_err("ERROR - No output annotation file from Blast2GO")
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
parents:
diff changeset
169
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peterjc
parents:
diff changeset
170 #Move the output file where Galaxy expects it to be:
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
peterjc
parents:
diff changeset
171 os.rename(out_file, tabular_file)
e4419efbefad Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
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parents:
diff changeset
172
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parents:
diff changeset
173 print "Done"