seriesoftubes.fnparsers

implements FilenameParsers for scripter

class seriesoftubes.fnparsers.BowtieFilenameParser(filename, *args, **kwargs)

check_paired_end()

tmp_filename(ref, match_type=None)

class seriesoftubes.fnparsers.BarcodeFilenameParser(filename, verbose=False, *args, **kwargs)

output_filename(barcode, is_barcode=True, no_gzip=False)

output_filename2(barcode, is_barcode=True, no_gzip=False)

class seriesoftubes.fnparsers.BAMFilenameParser(filename, controls={}, *args, **kwargs)

for alignments produced by align.py

class seriesoftubes.fnparsers.PeaksFilenameParser(filename, include_width_in_name=False, target=None, motif_file='unknown_motif', genome=None, *args, **kwargs)