Commit affb6437 authored by Claire Kuchly's avatar Claire Kuchly
Browse files

concatenate fastq for casava directory analyse

parent ed6713e6
......@@ -34,15 +34,23 @@ class IlluminaMatePair (NG6Workflow):
# manage the sequences files
group_prefix = None
print self.args['files_read']
print self.args['sample_description']['lane_number']
print self.project.get_name()
print self.args['sample_description']['casava_directory']
print "---------------------"
if self.args['sample_description']['casava_directory'] is not None :
if self.args['sample_description']['lane_number'] is None :
raise ValueError, "lane-number must be specified with casava-directory."
mids_desc_array, self.read1_files, self.read2_files = Utils.filesFromCasava( self.args['sample_description']['casava_directory'], self.project.get_name(), self.args['sample_description']['lane_number'] )
mids_desc_array, self.read1_files, self.read2_files, undetermined_read1_files, undetermined_read2_files = Utils.filesFromCasava( self.args['sample_description']['casava_directory'], self.project.get_name(), self.args['sample_description']['lane_number'] )
#print mids_desc_array, self.read1_files, self.read2_files, undetermined_read1_files, undetermined_read2_files
group_prefix = (Utils.get_group_basenames(self.read1_files+self.read2_files, "read")).keys()
self.runobj.add_mids_description(mids_desc_array)
# statistics about demultiplexing
if len(undetermined_read1_files) > 0 :
demultiplex_stats = self.add_component("DemultiplexStats", [self.read1_files, undetermined_read1_files])
elif (self.args['files_read'][0]['read_1'] is not None) and (len(self.args['files_read'][0]['read_1']) > 0) :
print self.args['files_read'][0]
self.read1_files = []
......@@ -101,7 +109,10 @@ class IlluminaMatePair (NG6Workflow):
contamination_search = self.add_component("ContaminationSearch", [filtered_read1_files+filtered_read2_files, self.args["databank"], reads_prefixes], parent = fastqilluminafilter)
# mate_pair analyse
cutadapt = self.add_component("CutAdapt",[filtered_read1_files,filtered_read2_files,{"g":["CTGTCTCTT","ATACACATCT","AGATCTAT","AAGAGACAG"]},{"g":["CTGTCTCTT","ATACACATCT","AGATCTAT","AAGAGACAG"]},is_paired_end,0.1,4,20 ],parent= fastqilluminafilter)
concatenate1 = self.add_component("ConcatenateFilesGroups", [filtered_read1_files, (Utils.get_group_basenames(self.read1_files, "read")).keys()],component_prefix="read1")
concatenate2 = self.add_component("ConcatenateFilesGroups", [filtered_read2_files, (Utils.get_group_basenames(self.read2_files, "read")).keys()],component_prefix="read2")
cutadapt = self.add_component("CutAdapt",[concatenate1.concat_files, concatenate2.concat_files,{"g":["CTGTCTCTT","ATACACATCT","AGATCTAT","AAGAGACAG"]},{"g":["CTGTCTCTT","ATACACATCT","AGATCTAT","AAGAGACAG"]},is_paired_end,0.1,4,20 ],parent= fastqilluminafilter)
#reverse_complement
......
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