annotate cuffdata.py @ 7:b5562b9a55c7

Use same bias_correction cached param as devteam cuffdiff
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 09:12:47 -0500
parents 137aab1d9ac1
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1 """
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2 CuffData
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3 """
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4 import logging
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5 import os,os.path,sys,re
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6 import tempfile
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7 from subprocess import Popen
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8 import galaxy.datatypes.data
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9 from galaxy.datatypes.images import Html
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10 from galaxy.datatypes.binary import Binary
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11 from galaxy import util
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12 from galaxy.datatypes.metadata import MetadataElement
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13
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14 log = logging.getLogger(__name__)
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15
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16 class CuffDiffData( Html ):
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17 """
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18 CuffDiff output files:
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19 run.info
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20 read_groups.info
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21 cds.count_tracking
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22 cds.diff
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23 cds.fpkm_tracking
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24 cds.read_group_tracking
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25 cds_exp.diff
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26 gene_exp.diff
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27 genes.count_tracking
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28 genes.fpkm_tracking
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29 genes.read_group_tracking
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30 isoform_exp.diff
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31 isoforms.count_tracking
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32 isoforms.fpkm_tracking
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33 isoforms.read_group_tracking
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34 promoters.diff
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35 splicing.diff
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36 tss_group_exp.diff
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37 tss_groups.count_tracking
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38 tss_groups.fpkm_tracking
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39 tss_groups.read_group_tracking
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40 """
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41 file_ext = 'cuffdata'
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42 is_binary = False
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43 composite_type = 'auto_primary_file'
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44 allow_datatype_change = False
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45 def __init__( self, **kwd ):
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46 Html.__init__( self, **kwd )
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47 self.add_composite_file('run.info', description = 'run.info', mimetype = 'text/html', optional = True, is_binary = False )
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48 self.add_composite_file('read_groups.info', description = 'read_groups.info', mimetype = 'text/html', optional = True, is_binary = False )
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49 self.add_composite_file('cds.count_tracking', description = 'cds.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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50 self.add_composite_file('cds.diff', description = 'cds.diff', mimetype = 'text/html', optional = True, is_binary = False )
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51 self.add_composite_file('cds.fpkm_tracking', description = 'cds.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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52 self.add_composite_file('cds.read_group_tracking', description = 'cds.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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53 self.add_composite_file('cds_exp.diff', description = 'cds_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
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54 self.add_composite_file('gene_exp.diff', description = 'gene_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
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55 self.add_composite_file('genes.count_tracking', description = 'genes.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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56 self.add_composite_file('genes.fpkm_tracking', description = 'genes.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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57 self.add_composite_file('genes.read_group_tracking', description = 'genes.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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58 self.add_composite_file('isoform_exp.diff', description = 'isoform_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
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59 self.add_composite_file('isoforms.count_tracking', description = 'isoforms.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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60 self.add_composite_file('isoforms.fpkm_tracking', description = 'isoforms.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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61 self.add_composite_file('isoforms.read_group_tracking', description = 'isoforms.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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62 self.add_composite_file('promoters.diff', description = 'promoters.diff', mimetype = 'text/html', optional = True, is_binary = False )
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63 self.add_composite_file('splicing.diff', description = 'splicing.diff', mimetype = 'text/html', optional = True, is_binary = False )
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64 self.add_composite_file('tss_group_exp.diff', description = 'tss_group_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
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65 self.add_composite_file('tss_groups.count_tracking', description = 'tss_groups.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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66 self.add_composite_file('tss_groups.fpkm_tracking', description = 'tss_groups.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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67 self.add_composite_file('tss_groups.read_group_tracking', description = 'tss_groups.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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68
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69 def generate_primary_file( self, dataset = None ):
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70 """
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71 This is called only at upload to write the html file
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72 cannot rename the datasets here - they come with the default unfortunately
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73 """
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74 rval = ['<html><head><title>CuffDiff Output</title></head>']
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75 rval.append('<body>')
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76 rval.append('<p/>CuffDiff Outputs:<p/><ul>')
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77 for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
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78 fn = composite_name
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79 log.debug( "Velvet log info %s %s %s" % ('JJ generate_primary_file',fn,composite_file))
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80 opt_text = ''
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81 if composite_file.optional:
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82 opt_text = ' (optional)'
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83 if composite_file.get('description'):
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84 rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
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85 else:
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86 rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) )
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87 rval.append( '</ul></body></html>' )
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88 return "\n".join( rval )
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89
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90 def regenerate_primary_file(self,dataset):
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91 """
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92 cannot do this until we are setting metadata
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93 """
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94 flist = os.listdir(dataset.extra_files_path)
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95 rval = ['<html><head><title>CuffDiff Output</title></head>']
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96 rval.append('<body>')
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97 rval.append('<p/>CuffDiff Outputs:<p/><ul>')
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98 for i,fname in enumerate(flist):
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99 sfname = os.path.split(fname)[-1]
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100 rval.append( '<li><a href="%s" type="text/html">%s</a>' % ( sfname, sfname ) )
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101 rval.append( '</ul></body></html>' )
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102 f = file(dataset.file_name,'w')
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103 f.write("\n".join( rval ))
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104 f.write('\n')
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105 f.close()
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106
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107 def set_meta( self, dataset, **kwd ):
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108 Html.set_meta( self, dataset, **kwd )
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109 self.regenerate_primary_file(dataset)
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110
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111 def sniff( self, filename ):
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112 return False
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113
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114 class CuffDataDB( Binary ):
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115 file_ext = 'cuffdatadb'
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116 is_binary = True
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117 allow_datatype_change = False
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118 MetadataElement( name="sample_names", default=[], desc="Sample names", readonly=True, visible=True, optional=True, no_value=[] )
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119 MetadataElement( name="replicate_names", default=[], desc="Replicate names", readonly=True, visible=True, optional=True, no_value=[] )
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120 MetadataElement( name="gene_ids", default=[], desc="Gene Ids", readonly=True, visible=True, optional=True, no_value=[] )
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121
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122 def __init__( self, **kwd ):
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123 Binary.__init__( self, **kwd )
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124 log.info('Creating cummeRbund CuffDataDB')
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125
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126 def set_meta( self, dataset, **kwd ):
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127 def get_contents(fname):
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128 contents = ''
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129 with open(fname,'r') as fh:
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130 contents = fh.read()
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131 return contents
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132 if not dataset.has_data():
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133 return
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134 try:
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135 ## Create a tmpdir
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136 ## create an Rscript to write out info about the CuffData, e.g. samples replicates gene_ids
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137 ## define file names to use as sinks for each type of data
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138 tmp_dir = tempfile.mkdtemp()
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139 if not os.path.isdir(tmp_dir):
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140 os.makedirs(tmp_dir)
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141 rscript = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.r' ).name
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142 rscript_fh = open( rscript, 'wb' )
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143 rscript_fh.write('library(cummeRbund)\n')
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144 rscript_fh.write('cuff<-readCufflinks(dir = "", dbFile = "%s", rebuild = F)\n' % (dataset.file_name))
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145 rscript_fh.write('sink("%s")\n' % ("out.blurb"))
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146 rscript_fh.write('print(cuff)\n')
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147 rscript_fh.write('sink()\n')
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148 rscript_fh.write('sink("%s")\n' % ("out.samples"))
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149 rscript_fh.write('cat(samples(cuff)[[2]],sep=",")\n')
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150 rscript_fh.write('sink()\n')
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151 rscript_fh.write('sink("%s")\n' % ("out.replicates"))
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152 rscript_fh.write('cat(replicates(cuff)[[4]],sep=",")\n')
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153 rscript_fh.write('sink()\n')
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154 rscript_fh.write('sink("%s")\n' % ("out.gene_ids"))
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155 rscript_fh.write('cat(annotation(genes(cuff))[[1]],sep=",")\n')
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156 rscript_fh.write('sink()\n')
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157 rscript_fh.close()
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158 cmd = ( "Rscript --vanilla %s" % rscript )
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159 tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
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160 tmp_stderr = open( tmp_stderr_name, 'wb' )
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161 proc = Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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162 returncode = proc.wait()
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163 tmp_stderr.close()
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164 flist = os.listdir(tmp_dir)
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165 for i,fname in enumerate(flist):
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166 sfname = os.path.split(fname)[-1]
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167 if sfname == 'out.blurb':
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168 dataset.blurb = get_contents(os.path.join(tmp_dir,fname))
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169 elif sfname == 'out.samples':
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170 dataset.metadata.sample_names = get_contents(os.path.join(tmp_dir,fname)).split(',')
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171 elif sfname == 'out.replicates':
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172 dataset.metadata.replicate_names = get_contents(os.path.join(tmp_dir,fname)).split(',')
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173 elif sfname == 'out.gene_ids':
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174 dataset.metadata.gene_ids = get_contents(os.path.join(tmp_dir,fname)).split(',')
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175 except Exception, e:
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176 log.error('Error setting cummeRbund CuffDataDB metadata : %s' % str(e))
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177