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 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)