def cmd():
if input_filename.endswith('.csv') or input_filename.endswith('.tsv'):
it = pd.read_csv(input_filename, chunksize=10000)
else:
it = maf.MafParser(input_filename)
with open(output_filename, 'a') as fp:
for group in it:
gff_group = gff.maf_to_gff3_df(group, database=database)
gff.write_gff3_df(gff_group, fp)
def cmd():
if input_filename.endswith('.csv') or input_filename.endswith('.tsv'):
it = pd.read_csv(input_filename, chunksize=10000)
else:
it = maf.MafParser(input_filename)
with open(output_filename, 'a') as fp:
for group in it:
gff_group = gff.maf_to_gff3_df(group, database=database)
gff.write_gff3_df(gff_group, fp)
def cmd():
with open(output_filename, 'a') as fp:
for group in parsers.cmscan_to_df_iter(input_filename):
gff_group = gff.cmscan_to_gff3_df(group, 'dammit.cmscan',
database)
gff.write_gff3_df(gff_group, fp)
def cmd():
with open(output_filename, 'a') as fp:
for group in parsers.cmscan_to_df_iter(input_filename):
gff_group = gff.cmscan_to_gff3_df(group, database=database)
gff.write_gff3_df(gff_group, fp)
def cmd():
with open(output_filename, 'a') as fp:
for group in pd.read_csv(input_filename, chunksize=10000):
gff_group = gff.hmmscan_to_gff3_df(group, database=database)
gff.write_gff3_df(gff_group, fp)
def cmd():
with open(output_filename, 'a') as fp:
for group in pd.read_csv(input_filename, chunksize=10000):
gff_group = gff.hmmscan_to_gff3_df(group, database=database)
gff.write_gff3_df(gff_group, fp)
def cmd():
with open(output_filename, 'a') as fp:
for group in parsers.crb_to_df_iter(input_filename,
remap=True):
gff_group = gff.crb_to_gff3_df(group, database=database)
gff.write_gff3_df(gff_group, fp)
def cmd():
with open(output_filename, 'a') as fp:
for group in parsers.crb_to_df_iter(input_filename, remap=True):
gff_group = gff.crb_to_gff3_df(group, 'dammit.crbb', database)
gff.write_gff3_df(gff_group, fp)
