Mercurial > repos > peterjc > blast2go

annotate tools/ncbi_blast_plus/blast2go.py @ 2:5cb24d07c316 draft

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Uploaded v0.0.4 with explicit dependency on 'blast_datatypes' for 'blastxml' format definition. No functional changes.
author peterjc
date Fri, 22 Feb 2013 09:13:27 -0500
parents 7b53cc52e7ed
children
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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:
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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
2
5cb24d07c316 Uploaded v0.0.4 with explicit dependency on 'blast_datatypes' for 'blastxml' format definition. No functional changes.
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9 Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current
5cb24d07c316 Uploaded v0.0.4 with explicit dependency on 'blast_datatypes' for 'blastxml' format definition. No functional changes.
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10 style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat
5cb24d07c316 Uploaded v0.0.4 with explicit dependency on 'blast_datatypes' for 'blastxml' format definition. No functional changes.
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11 these to avoid it crashing with a Java heap space OutOfMemoryError.
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12
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13 As part of this reformatting, we check for BLASTP or BLASTX output
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14 (otherwise raise an error), and print the query count.
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15
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16 It then calls the Java command line tool, and moves the output file to
1
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17 the location Galaxy is expecting, and removes the tempory XML file.
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18 """
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19 import sys
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20 import os
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21 import subprocess
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22
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23 #You may need to edit this to match your local setup,
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24 blast2go_jar = "/opt/b2g4pipe/blast2go.jar"
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26
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27 def stop_err(msg, error_level=1):
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28 """Print error message to stdout and quit with given error level."""
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29 sys.stderr.write("%s\n" % msg)
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30 sys.exit(error_level)
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31
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32 if len(sys.argv) != 4:
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33 stop_err("Require three arguments: XML filename, properties filename, output tabular filename")
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34
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35 xml_file, prop_file, tabular_file = sys.argv[1:]
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36
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37 #We should have write access here:
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38 tmp_xml_file = tabular_file + ".tmp.xml"
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39
0
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40 if not os.path.isfile(xml_file):
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41 stop_err("Input BLAST XML file not found: %s" % xml_file)
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42
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43 if not os.path.isfile(prop_file):
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44 stop_err("Blast2GO configuration file not found: %s" % prop_file)
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45
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46 def prepare_xml(original_xml, mangled_xml):
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47 """Reformat BLAST XML to suit Blast2GO.
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48
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49 Blast2GO can't cope with 1000s of <Iteration> tags within a
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50 single <BlastResult> tag, so instead split this into one
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51 full XML record per interation (i.e. per query). This gives
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52 a concatenated XML file mimicing old versions of BLAST.
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53
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54 This also checks for BLASTP or BLASTX output, and outputs
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55 the number of queries. Galaxy will show this as "info".
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56 """
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57 in_handle = open(original_xml)
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58 footer = " </BlastOutput_iterations>\n</BlastOutput>\n"
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59 header = ""
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60 while True:
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61 line = in_handle.readline()
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62 if not line:
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63 #No hits?
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64 stop_err("Problem with XML file?")
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65 if line.strip() == "<Iteration>":
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66 break
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67 header += line
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68
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69 if "<BlastOutput_program>blastx</BlastOutput_program>" in header:
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70 print "BLASTX output identified"
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71 elif "<BlastOutput_program>blastp</BlastOutput_program>" in header:
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72 print "BLASTP output identified"
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73 else:
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74 in_handle.close()
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75 stop_err("Expect BLASTP or BLASTX output")
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76
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77 out_handle = open(mangled_xml, "w")
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78 out_handle.write(header)
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79 out_handle.write(line)
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80 count = 1
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81 while True:
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82 line = in_handle.readline()
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83 if not line:
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84 break
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85 elif line.strip() == "<Iteration>":
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86 #Insert footer/header
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87 out_handle.write(footer)
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88 out_handle.write(header)
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89 count += 1
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90 out_handle.write(line)
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91
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92 out_handle.close()
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93 in_handle.close()
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94 print "Input has %i queries" % count
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95
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96
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97 def run(cmd):
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98 #Avoid using shell=True when we call subprocess to ensure if the Python
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99 #script is killed, so too is the child process.
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100 try:
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101 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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102 except Exception, err:
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103 stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
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104 #Use .communicate as can get deadlocks with .wait(),
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105 stdout, stderr = child.communicate()
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106 return_code = child.returncode
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107 if return_code:
1
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108 cmd_str = " ".join(cmd)
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109 if stderr and stdout:
1
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110 stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
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111 else:
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112 stop_err("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
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113 #For early diagnostics,
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114 else:
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115 print stdout
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116 print stderr
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117
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118 if not os.path.isfile(blast2go_jar):
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119 stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)
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120
1
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121 prepare_xml(xml_file, tmp_xml_file)
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122 #print "XML file prepared for Blast2GO"
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123
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124 #We will have write access wherever the output should be,
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125 #so we'll ask Blast2GO to use that as the stem for its output
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126 #(it will append .annot to the filename)
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127 cmd = ["java", "-jar", blast2go_jar,
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128 "-in", tmp_xml_file,
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129 "-prop", prop_file,
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130 "-out", tabular_file, #Used as base name for output files
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131 "-a", # Generate *.annot tabular file
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132 #"-img", # Generate images, feature not in v2.3.5
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133 ]
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134 #print " ".join(cmd)
0
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135 run(cmd)
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136
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137 #Remove the temp XML file
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138 os.remove(tmp_xml_file)
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139
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140 out_file = tabular_file + ".annot"
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141 if not os.path.isfile(out_file):
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142 stop_err("ERROR - No output annotation file from Blast2GO")
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143
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diff changeset
144 #Move the output file where Galaxy expects it to be:
4bfd64cf18ab 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)
4bfd64cf18ab Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
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146
4bfd64cf18ab Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
147 print "Done"