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()
