Mercurial > repos > dfornika > blast_report_basic

comparison blast_report.py @ 23:8d92b3b58f5e draft

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author dfornika
date Tue, 03 Mar 2020 09:30:07 +0000
parents 9cf35f30bfb4
children e2cab62e1943
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22:261235bbd475 23:8d92b3b58f5e
2 2
3 from __future__ import print_function 3 from __future__ import print_function
4 4
5 '''Report on BLAST results. 5 '''Report on BLAST results.
6 6
7 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]] 7 python blast_report.py input_tab cheetah_tmpl output_html output_tab [-i [min_identity]] [-f filterkw1,...,filterkwN]] [-b bin1_label=bin1_path[,...binN_label=binN_path]]
8 ''' 8 '''
9 9
10 import argparse 10 import argparse
11 import re 11 import re
12 import sys 12 import sys
13 13
14 from Cheetah.Template import Template 14 from Cheetah.Template import Template
15 15 from pprint import pprint
16 16
17 def stop_err( msg ): 17 def stop_err( msg ):
18 sys.stderr.write("%s\n" % msg) 18 sys.stderr.write("%s\n" % msg)
19 sys.exit(1) 19 sys.exit(1)
20 20
79 ) 79 )
80 parser.add_argument('-i', '--min-identity', 80 parser.add_argument('-i', '--min-identity',
81 dest='min_identity', 81 dest='min_identity',
82 ) 82 )
83 parser.add_argument('-b', '--bins', 83 parser.add_argument('-b', '--bins',
84 dest='bins' 84 dest='bins',
85 action='append',
86 nargs='+'
85 ) 87 )
86 parser.add_argument('-r', '--discard-redundant', 88 parser.add_argument('-r', '--discard-redundant',
87 dest='discard_redundant', 89 dest='discard_redundant',
88 default=False, 90 default=False,
89 action='store_true' 91 action='store_true'
90 ) 92 )
91 parser.add_argument('input_tab') 93 parser.add_argument('input_tab')
92 parser.add_argument('cheetah_tmpl') 94 parser.add_argument('cheetah_tmpl')
93 parser.add_argument('output_html') 95 parser.add_argument('output_html')
94 parser.add_argument('output_tab') 96 parser.add_argument('output_tab')
97
95 args = parser.parse_args() 98 args = parser.parse_args()
99
100 pprint(bins)
96 101
97 print('input_tab: %s cheetah_tmpl: %s output_html: %s output_tab: %s' % (args.input_tab, args.cheetah_tmpl, args.output_html, args.output_tab)) 102 print('input_tab: %s cheetah_tmpl: %s output_html: %s output_tab: %s' % (args.input_tab, args.cheetah_tmpl, args.output_html, args.output_tab))
98 103
99 104
100 #BINS 105 #BINS