Dear All,
I would like to understand how work this funcion:
def parse_illumina_readset_file(illumina_readset_file):
readsets = []
samples = []
log.info("Parse readset " + illumina_readset_file + " ...")
readset_csv = csv.DictReader(open(illumina_readset_file, 'rb'),
delimiter='\t')
for line in readset_csv:
sample_name = line['Sample']
sample_names = [sample.name for sample in samples]
if sample_name in sample_names:
# Sample already exists
sample = samples[sample_names.index(sample_name)]
else:
# Create new sample
sample = Sample(sample_name)
samples.append(sample)
# Create readset and add it to sample
readset = IlluminaReadset(line['Readset'], line['RunType'])
# Readset file paths are either absolute or relative to the readset file
# Convert them to absolute paths
for format in ("BAM", "FASTQ1", "FASTQ2"):
if line.get(format, None):
line[format] = os.path.expandvars(line[format])
if not os.path.isabs(line[format]):
line[format] =
os.path.dirname(os.path.abspath(os.path.expandvars(illumina_readset_file))) +
os.sep + line[format]
line[format] = os.path.normpath(line[format])
readset._bam = line.get('BAM', None)
readset.fastq1 = line.get('FASTQ1', None)
readset.fastq2 = line.get('FASTQ2', None)
readset._library = line.get('Library', None)
readset._run = line.get('Run', None)
readset._lane = line.get('Lane', None)
readset._adaptor1 = line.get('Adaptor1', None)
readset._adaptor2 = line.get('Adaptor2', None)
readset._quality_offset = int(line['QualityOffset']) if
line.get('QualityOffset', None) else None
readset._beds = line['BED'].split(";") if line.get('BED', None) else []
readsets.append(readset)
sample.add_readset(readset)
log.info(str(len(readsets)) + " readset" + ("s" if len(readsets) > 1 else
"") + " parsed")
log.info(str(len(samples)) + " sample" + ("s" if len(samples) > 1 else "")
+ " parsed\n")
return readsets
parser_illumina_readset_file("~/Desktop/file.csv")
dir()
I can't found the readsets list. Someone could please help me?
thanks so much!
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