except:
FASTQ_FILE_CREATED = 'N'
try:
BARCODE_ENTERED = sys.argv[10]
except:
BARCODE_ENTERED = 'none found'
try:
ONLY_FWD_READS = (sys.argv[11] == 'Y')
except:
ONLY_FWD_READS = False
data_to_display = True
msg_to_user = ""
if FASTQ_FILE_CREATED != 'N':
coverage = SamCoverage(GENOME)
transcript_names = []
transcript_sizes = []
with open(GENOME) as ercc_genome:
for line in ercc_genome:
parsed_line = line.split()
transcript_names.append(parsed_line[0])
transcript_sizes.append(parsed_line[1])
# write counts file and filtered sam file, return stats tuple
counts, all_ercc_counts, total_counts, mean_mapqs = write_output_counts_file(
RAW_SAM_FILE, FILTERED_SAM_FILE, COUNTS_FILE, transcript_names,
ONLY_FWD_READS)
if (total_counts > 0):
percent_total_counts_ercc = '%.2f' % (100 *
(all_ercc_counts / total_counts))
