comparison blast_report.py @ 3:386a88793078 draft

Uploaded

2:0dbaa4e68866

#!/usr/bin/env python
'''Report on BLAST results.

python blast_report.py input_tab cheetah_tmpl output_html output_tab [-f [filter_pident]:[filterkw1,...,filterkwN]] [-b bin1_label=bin1_path[,...binN_label=binN_path]]
'''
import argparse
import re
import sys

from Cheetah.Template import Template

#PARSE OPTIONS AND ARGUMENTS
parser = argparse.ArgumentParser()

parser.add_argument('-f', '--filter',
                    type='string',
                    dest='filter',
                    )
parser.add_argument('-b', '--bins',
                    type='string',
                    dest='bins'
                    )
parser.add_argument('-r', '--redundant',
                    dest='redundant',
                    default=False,
                    action='store_true'
                    )
args = parser.parse_args()

    pident_kws = args.filter.split(':')
    filter_pident = float(pident_kws[0])
    filter_kws = pident_kws[-1].split(',')
print('filter_pident: %s    filter_kws: %s' % (str(filter_pident), str(filter_kws)))

if args.redundant:
    print('Throwing out redundant hits...')

#RESULTS!
PIDENT_COL = 2
DESCR_COL = 25

            accs = cols[SUBJ_ID_COL].split('|')[1::2][1::2]
        except IndexError as e:
            stop_err("Problem with splitting:" + cols[SUBJ_ID_COL])

        #hsp option: keep best (first) hit only for each query and accession id.
        if args.redundant:
            if accs[0] in queries[-1].match_accessions:
                continue #don't save the result and skip to the next
            else:
                queries[-1].match_accessions[accs[0]] = ''

3:386a88793078

#!/usr/bin/env python

from __future__ import print_function

'''Report on BLAST results.

python blast_report.py input_tab cheetah_tmpl output_html output_tab [-f [filter_pident]:[filterkw1,...,filterkwN]] [-b bin1_label=bin1_path[,...binN_label=binN_path]]
'''

import argparse
import re
import sys

from Cheetah.Template import Template

#PARSE OPTIONS AND ARGUMENTS
parser = argparse.ArgumentParser()

parser.add_argument('-f', '--filter',
                    dest='filter',
                    )
parser.add_argument('-b', '--bins',
                    dest='bins'
                    )
parser.add_argument('-r', '--discard-redundant',
                    dest='discard_redundant',
                    type=bool,
                    default=False,
                    action='store_true'
                    )
args = parser.parse_args()

    pident_kws = args.filter.split(':')
    filter_pident = float(pident_kws[0])
    filter_kws = pident_kws[-1].split(',')
print('filter_pident: %s    filter_kws: %s' % (str(filter_pident), str(filter_kws)))

if args.discard_redundant:
    print('Throwing out redundant hits...')

#RESULTS!
PIDENT_COL = 2
DESCR_COL = 25

            accs = cols[SUBJ_ID_COL].split('|')[1::2][1::2]
        except IndexError as e:
            stop_err("Problem with splitting:" + cols[SUBJ_ID_COL])

        #hsp option: keep best (first) hit only for each query and accession id.
        if args.discard_redundant:
            if accs[0] in queries[-1].match_accessions:
                continue #don't save the result and skip to the next
            else:
                queries[-1].match_accessions[accs[0]] = ''