assign_taxonomy_by_blast _result.py

Assign taxonomy to a rep set of OTUs that were chosen by BLAST from an annotated database.

usage: assign_taxonomy_by_blast_result.py [-h] -i REP_SET_FP -t ID_TO_TAXONOMY_FP [-o ASSIGNED_TAXONOMY_FP] [-v]

Required arguments

-i REP_SET_FP, --rep_set_fp REP_SET_FP

The set of representative sequences.

-t ID_TO_TAXONOMY_FP, --id_to_taxonomy_fp ID_TO_TAXONOMY_FP

Path to tab-delimited file mapping sequences to assigned taxonomy.

Optional arguments

-o ASSIGNED_TAXONOMY_FP, --assigned_taxonomy_fp ASSIGNED_TAXONOMY_FP

The path to the result file. By default outputs to assigned_taxonomy.txt

-h, --help

Show the help message and exit

-v, --verbose

Print detailed information about script operation.