Mercurial > repos > dfornika > blast_report_basic

comparison blast_report.py @ 26:e2cab62e1943 draft

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Uploaded
author dfornika
date Tue, 03 Mar 2020 09:57:34 +0000
parents 8d92b3b58f5e
children 7caa67bdcdf0
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25:d29bf2f7da9d 26:e2cab62e1943
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 [-i [min_identity]] [-f 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
103 103
104 104
105 #BINS 105 #BINS
106 bins=[] 106 bins=[]
107 if args.bins != None: 107 if args.bins != None:
108 bins = list([BLASTBin(label_file.split('=')[0],label_file.split('=')[-1]) for label_file in args.bins.split(',')]) 108 for bin in args.bins:
109 bins.append(BLASTBin(bin[0], bin[1])
110
109 print('database bins: %s' % str([bin.label for bin in bins])) 111 print('database bins: %s' % str([bin.label for bin in bins]))
110 112
111 #FILTERS 113 #FILTERS
112 filter_pident = 0 114 filter_pident = 0
113 filter_kws = [] 115 filter_kws = []