[Tutor] How to use a function

[Albert-Jan Roskam]

----------------------------
On Mon, Jan 19, 2015 3:32 PM CET jarod_v6 at 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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