Python hmmscan_to_gff3_df Examples

Example #1

File: tasks.py Project: macmanes-lab/dammit

 def cmd():
     with open(output_filename, 'a') as fp:
         for group in parsers.hmmscan_to_df_iter(input_filename):
             gff_group = gff.hmmscan_to_gff3_df(group, 'dammit.hmmscan',
                                                database)
             gff.write_gff3_df(gff_group, fp)

Example #2

File: tasks.py Project: camillescott/dammit

 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)

Example #3

 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)

Example #4

File: tasks.py Project: macmanes/dammit

 def cmd():
     with open(output_filename, 'a') as fp:
         for group in parsers.hmmscan_to_df_iter(input_filename):
             gff_group = gff.hmmscan_to_gff3_df(group, 'dammit.hmmscan',
                                                database)
             gff.write_gff3_df(gff_group, fp)