Python _prepare_quality_parameter Exemples

Exemple #1

 def run(self, args):
     quality = gem._prepare_quality_parameter(args.quality)
     raw = False
     if args.input is not None:
         map_file = gem.files.open(args.input, quality=quality)
     else:
         map_file = gem.files.open(sys.stdin, quality=quality)
         raw = True
     cons = gem.extended_splice_consensus
     if args.no_xs:
         cons = None
     sam = gem.gem2sam(map_file,
                         index=args.index,
                         threads=args.threads,
                         quality=args.quality,
                         consensus=cons,
                         raw=raw
                         )
     gem.sam2bam(sam, output=args.output,
                 sorted=not args.no_sort,
                 threads=args.threads,
                 sort_memory=str(args.sort_memory))
     if not args.no_index:
         gem.bamIndex(args.output)

Exemple #2

Fichier : parameter_converter_tests.py Projet : MarcosFernandez/gemtools-cnv

def test_quality_parameter():
    assert gem._prepare_quality_parameter(None) == 'ignore'
    assert gem._prepare_quality_parameter(33) == 'offset-33'
    assert gem._prepare_quality_parameter(64) == 'offset-64'

Exemple #3

Fichier : parameter_converter_tests.py Projet : yesimon/gemtools

def test_quality_parameter():
    assert gem._prepare_quality_parameter(None) == 'ignore'
    assert gem._prepare_quality_parameter(33) == 'offset-33'
    assert gem._prepare_quality_parameter(64) == 'offset-64'