----------------------------
On Mon, Jan 19, 2015 3:32 PM CET jarod...@libero.it wrote:
>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")
Too much code to read ony tiny phone screen, but I think you also need to wrap
the filename in os.pat.expanduser to get tilde expansion.
>dir()
>
>I can't found the readsets list. Someone could please help me?
>thanks so much!
>
>
>
>
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