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annotate datamanager_create_reference.py @ 26:8f0775c43739

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Fix metadata_source in defuse_results_to_vcf.xml
author Jim Johnson <jj@umn.edu>
date Fri, 09 Aug 2013 11:36:24 -0500
parents b649c729be4c
children
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1 #!/usr/bin/env python
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2
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3 import sys
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4 import os
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5 import re
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6 import tempfile
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7 import subprocess
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8 import fileinput
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9 import shutil
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10 import optparse
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11 import urllib2
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12 from ftplib import FTP
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13 import tarfile
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14
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15 from galaxy.util.json import from_json_string, to_json_string
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16
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17
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18 def stop_err(msg):
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19 sys.stderr.write(msg)
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20 sys.exit(1)
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21
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22 def get_config_dict(config,dataset_directory=None):
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23 keys = ['dataset_directory','ensembl_organism','ensembl_prefix','ensembl_version','ensembl_genome_version','ucsc_genome_version','ncbi_organism','ncbi_prefix','chromosomes','mt_chromosome','gene_sources','ig_gene_sources','rrna_gene_sources']
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24 pat = '^([^=]+?)\s*=\s*(.*)$'
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25 config_dict = {}
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26 try:
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27 fh = open(config)
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28 for i,l in enumerate(fh):
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29 line = l.strip()
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30 if line.startswith('#'):
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31 continue
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32 m = re.match(pat,line)
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33 if m and len(m.groups()) == 2:
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34 (k,v) = m.groups()
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35 if k in keys:
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36 config_dict[k] = v
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37 except Exception, e:
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38 stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
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39 else:
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40 fh.close()
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41 if dataset_directory:
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42 config_dict['dataset_directory'] = dataset_directory
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43 return config_dict
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44
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45 def run_defuse_script(data_manager_dict, params, target_directory, dbkey, description, config, script):
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46 if not os.path.isdir(target_directory):
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47 os.makedirs(target_directory)
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48 ## Name the config consistently with data_manager_conf.xml
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49 # copy the config file to the target_directory
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50 # when DataManager moves files to there tool-data location, the config will get moved as well,
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51 # and the value_translation in data_manager_conf.xml will tell us the new location
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52 # defuse.xml will use the path to this config file to set the dataset_directory
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53 config_name = '%s.config' % dbkey
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54 defuse_config = os.path.join( target_directory, config_name)
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55 shutil.copyfile(config,defuse_config)
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56 cmd = "/bin/bash %s %s" % (script,target_directory)
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57 # Run
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58 try:
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59 tmp_out = tempfile.NamedTemporaryFile().name
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60 tmp_stdout = open( tmp_out, 'wb' )
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61 tmp_err = tempfile.NamedTemporaryFile().name
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62 tmp_stderr = open( tmp_err, 'wb' )
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63 proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
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64 returncode = proc.wait()
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65 tmp_stderr.close()
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66 # get stderr, allowing for case where it's very large
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67 tmp_stderr = open( tmp_err, 'rb' )
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68 stderr = ''
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69 buffsize = 1048576
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70 try:
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71 while True:
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72 stderr += tmp_stderr.read( buffsize )
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73 if not stderr or len( stderr ) % buffsize != 0:
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74 break
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75 except OverflowError:
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76 pass
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77 tmp_stdout.close()
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78 tmp_stderr.close()
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79 if returncode != 0:
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80 raise Exception, stderr
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81
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82 # TODO: look for errors in program output.
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83 except Exception, e:
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84 stop_err( 'Error creating defuse reference:\n' + str( e ) )
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85 config_dict = get_config_dict(config, dataset_directory=target_directory)
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86 data_table_entry = dict(value=dbkey, dbkey=dbkey, name=description, path=config_name)
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87 _add_data_table_entry( data_manager_dict, data_table_entry )
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88 def _add_data_table_entry( data_manager_dict, data_table_entry ):
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89 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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90 data_manager_dict['data_tables']['defuse_reference'] = data_manager_dict['data_tables'].get( 'defuse_reference', [] )
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91 data_manager_dict['data_tables']['defuse_reference'].append( data_table_entry )
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92 return data_manager_dict
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93
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94 def main():
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95 #Parse Command Line
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96 parser = optparse.OptionParser()
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97 parser.add_option( '-k', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='dbkey' )
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98 parser.add_option( '-d', '--description', dest='description', action='store', type="string", default=None, help='description' )
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99 parser.add_option( '-c', '--defuse_config', dest='defuse_config', action='store', type="string", default=None, help='defuse_config' )
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100 parser.add_option( '-s', '--defuse_script', dest='defuse_script', action='store', type="string", default=None, help='defuse_script' )
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101 (options, args) = parser.parse_args()
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102
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103 filename = args[0]
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104
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105 params = from_json_string( open( filename ).read() )
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106 target_directory = params[ 'output_data' ][0]['extra_files_path']
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107 os.mkdir( target_directory )
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108 data_manager_dict = {}
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109
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110
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111 #Create Defuse Reference Data
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112 run_defuse_script( data_manager_dict, params, target_directory, options.dbkey, options.description,options.defuse_config,options.defuse_script)
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113
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114 #save info to json file
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115 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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116
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117 if __name__ == "__main__": main()
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118