def _populate_barcode_info_from_conversion_file(self, conversion_xml_file):
all_barcodes_per_lanes, top_unknown_barcodes_per_lanes = parse_conversion_stats(conversion_xml_file)
for project, library, lane, barcode, clust_count, clust_count_pf, nb_bases,\
nb_bases_r1q30, nb_bases_r2q30, in all_barcodes_per_lanes:
barcode_info = self.barcodes_info.get('%s_%s_%s'%(self.run_id, lane, barcode))
barcode_info[ELEMENT_NB_READS_SEQUENCED]=int(clust_count)
barcode_info[ELEMENT_NB_READS_PASS_FILTER]=int(clust_count_pf)
#For the paired end reads
barcode_info[ELEMENT_NB_BASE_R1]=int(nb_bases)
barcode_info[ELEMENT_NB_BASE_R2]=int(nb_bases)
barcode_info[ELEMENT_NB_Q30_R1]=int(nb_bases_r1q30)
barcode_info[ELEMENT_NB_Q30_R2]=int(nb_bases_r2q30)
for lane, barcode, clust_count in top_unknown_barcodes_per_lanes:
barcode_info = Info()
barcode_info[ELEMENT_RUN_ELEMENT_ID] = '%s_%s_%s'%(self.run_id, lane, barcode)
barcode_info[ELEMENT_RUN_NAME]=self.run_id
barcode_info[ELEMENT_LANE]=lane
barcode_info[ELEMENT_BARCODE]=barcode
barcode_info[ELEMENT_NB_READS_PASS_FILTER]=int(clust_count)
self.unexpected_barcode_info[barcode_info[ELEMENT_RUN_ELEMENT_ID]]=(barcode_info)
def test_parse_conversion_stats(self):
all_barcodes_per_lanes, top_unknown_barcodes_per_lanes = parse_conversion_stats(self.xml_file2)
self.assertTrue(all_barcodes_per_lanes)
self.assertTrue(top_unknown_barcodes_per_lanes)
