comparison kraken_taxonomy_report.py @ 2:528a1d91b066 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0

1:b97694b21bc3

# Licensed under the Academic Free License version 3.0
# https://github.com/blankenberg/Kraken-Taxonomy-Report

from __future__ import print_function

import sys
import os
import optparse
import re

__VERSION__ = '0.0.2'

__URL__ = "https://github.com/blankenberg/Kraken-Taxonomy-Report"

    else:
        options.cluster = None  # make empty string into None
        ranks_to_report = RANK_NAMES_INTS

    if options.output:
        output_fh = open( options.output, 'wb+' )
    else:
        output_fh = sys.stdout

    db_path = get_kraken_db_path( options.db )
    ( child_lists, name_map, rank_map ) = load_taxonomy( db_path, sanitize_names=options.sanitize_names )

2:528a1d91b066

# Licensed under the Academic Free License version 3.0
# https://github.com/blankenberg/Kraken-Taxonomy-Report

from __future__ import print_function

import optparse
import os
import re
import sys

__VERSION__ = '0.0.2'

__URL__ = "https://github.com/blankenberg/Kraken-Taxonomy-Report"

    else:
        options.cluster = None  # make empty string into None
        ranks_to_report = RANK_NAMES_INTS

    if options.output:
        output_fh = open(options.output, 'w')
    else:
        output_fh = sys.stdout

    db_path = get_kraken_db_path( options.db )
    ( child_lists, name_map, rank_map ) = load_taxonomy( db_path, sanitize_names=options.sanitize_names )