def ___fai2genome(self): """Process existing fasta index, depends from 'samtools_faidx' function""" def ____parse_fai_line(split_line: list): if len(split_line) >= 2: return split_line[:2] print("Bad FAI file line: {}".format("\t".join(split_line))) fai_2d_array = Utilities.load_2d_array("{}_samtools.fai".format(self._reference_mask)) genome_2d_array = [] for line in fai_2d_array: genome_2d_array.append(____parse_fai_line(line)) out = "{}_samtools.genome".format(self._reference_mask) Utilities.dump_2d_array(array=Utilities.remove_empty_values(genome_2d_array), file=out) print("Created BEDTools genome index: '{}'".format(out))
def __init__(self): self._queue = Utilities.load_2d_array(mainInitializer.sampledata) self._verified_df = pd.DataFrame() self._no_coverages_df = pd.DataFrame()