Mercurial > repos > dfornika > blast_report

annotate blast_report.py @ 2:cf3e9a68d558 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit e8b469f0fed66159f07bfc3904b0c4bce9a16d09-dirty
author dfornika
date Wed, 11 Sep 2019 23:34:31 -0400
parents 18b097eb1a51
children 2b4f30c6b50a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
1 #!/usr/bin/env python
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
2 from __future__ import print_function
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
3
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
4 '''Report on BLAST results.
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
5
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
6 python bccdc_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]]
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
7 '''
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
8
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
9 import optparse
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
10 import re
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
11 import sys
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
12
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
13 def stop_err( msg ):
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
14 sys.stderr.write("%s\n" % msg)
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
15 sys.exit(1)
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
16
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
17 class BLASTBin:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
18 def __init__(self, label, file):
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
19 self.label = label
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
20 self.dict = {}
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
21
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
22 file_in = open(file)
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
23 for line in file_in:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
24 self.dict[line.rstrip().split('.')[0]] = ''
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
25 file_in.close()
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
26
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
27 def __str__(self):
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
28 return "label: %s dict: %s" % (self.label, str(self.dict))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
29
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
30 class BLASTQuery:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
31 def __init__(self, query_id):
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
32 self.query_id = query_id
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
33 self.matches = []
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
34 self.match_accessions = {}
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
35 self.bins = {} #{bin(label):[match indexes]}
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
36 self.pident_filtered = 0
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
37 self.kw_filtered = 0
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
38 self.kw_filtered_breakdown = {} #{kw:count}
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
39
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
40 def __str__(self):
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
41 return "query_id: %s len(matches): %s bins (labels only): %s pident_filtered: %s kw_filtered: %s kw_filtered_breakdown: %s" \
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
42 % (self.query_id,
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
43 str(len(self.matches)),
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
44 str([bin.label for bin in bins]),
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
45 str(self.pident_filtered),
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
46 str(self.kw_filtered),
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
47 str(self.kw_filtered_breakdown))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
48
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
49 class BLASTMatch:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
50 def __init__(self, subject_acc, subject_descr, score, p_cov, p_ident, subject_bins):
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
51 self.subject_acc = subject_acc
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
52 self.subject_descr = subject_descr
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
53 self.score = score
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
54 self.p_cov = p_cov
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
55 self.p_ident = p_ident
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
56 self.bins = subject_bins
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
57
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
58 def __str__(self):
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
59 return "subject_acc: %s subject_descr: %s score: %s p-cov: %s p-ident: %s" \
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
60 % (self.subject_acc,
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
61 self.subject_descr,
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
62 str(self.score),
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
63 str(round(self.p_cov,2)),
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
64 str(round(self.p_ident, 2)))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
65
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
66 #PARSE OPTIONS AND ARGUMENTS
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
67 parser = optparse.OptionParser(description='Report on BLAST results.',
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
68 usage='python bccdc_blast_report_generator.py input_tabut cheetah_tmpl output_html [output_id output_dir] [options]')
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
69
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
70 parser.add_option('-f', '--filter',
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
71 type='string',
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
72 dest='filter',
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
73 )
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
74 parser.add_option('-b', '--bins',
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
75 type='string',
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
76 dest='bins'
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
77 )
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
78 parser.add_option('-r', '--redundant',
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
79 dest='hsp',
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
80 default=False,
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
81 action='store_true'
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
82 )
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
83 options, args = parser.parse_args()
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
84
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
85 try:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
86 input_tab, cheetah_tmpl, output_html, output_tab = args
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
87 except:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
88 stop_err('you must supply the arguments input_tab, cheetah_tmpl and output_html.')
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
89 #print('input_tab: %s cheetah_tmpl: %s output_html: %s output_tab: %s' % (input_tab, cheetah_tmpl, output_html, output_tab))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
90
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
91 #BINS
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
92 bins=[]
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
93 if options.bins != None:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
94 bins = list([BLASTBin(label_file.split('=')[0],label_file.split('=')[-1]) for label_file in options.bins.split(',')])
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
95 print('database bins: %s' % str([bin.label for bin in bins]))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
96
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
97 #FILTERS
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
98 filter_pident = 0
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
99 filter_kws = []
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
100 if options.filter != None:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
101 pident_kws = options.filter.split(':')
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
102 filter_pident = float(pident_kws[0])
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
103 filter_kws = pident_kws[-1].split(',')
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
104 print('filter_pident: %s filter_kws: %s' % (str(filter_pident), str(filter_kws)))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
105
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
106 if options.hsp:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
107 print('Throwing out redundant hits...')
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
108
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
109 #RESULTS!
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
110 PIDENT_COL = 2
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
111 DESCR_COL = 25
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
112 SUBJ_ID_COL = 12
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
113 SCORE_COL = 11
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
114 PCOV_COL = 24
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
115 queries = []
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
116 current_query = ''
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
117 output_tab = open(output_tab, 'w')
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
118 with open(input_tab) as input_tab:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
119 for line in input_tab:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
120 cols = line.split('\t')
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
121 if cols[0] != current_query:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
122 current_query = cols[0]
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
123 queries.append(BLASTQuery(current_query))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
124
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
125 try:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
126 accs = cols[SUBJ_ID_COL].split('|')[1::2][1::2]
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
127 except IndexError as e:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
128 stop_err("Problem with splitting:" + cols[SUBJ_ID_COL])
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
129
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
130 #hsp option: keep best (first) hit only for each query and accession id.
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
131 if options.hsp:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
132 if accs[0] in queries[-1].match_accessions:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
133 continue #don't save the result and skip to the next
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
134 else:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
135 queries[-1].match_accessions[accs[0]] = ''
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
136
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
137
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
138 p_ident = float(cols[PIDENT_COL])
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
139 #FILTER BY PIDENT
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
140 if p_ident < filter_pident: #if we are not filtering, filter_pident == 0 and this will never evaluate to True
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
141 queries[-1].pident_filtered += 1
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
142 continue
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
143
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
144 descrs = cols[DESCR_COL]
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
145 #FILTER BY KEY WORDS
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
146 filter_by_kw = False
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
147 for kw in filter_kws:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
148 kw = kw.strip() #Fix by Damion D Nov 2013
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
149 if kw != '' and re.search(kw, descrs, re.IGNORECASE):
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
150 filter_by_kw = True
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
151 try:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
152 queries[-1].kw_filtered_breakdown[kw] += 1
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
153 except:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
154 queries[-1].kw_filtered_breakdown[kw] = 1
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
155 if filter_by_kw: #if we are not filtering, for loop will not be entered and this will never be True
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
156 queries[-1].kw_filtered += 1
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
157 continue
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
158 descr = descrs.split(';')[0]
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
159
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
160 #ATTEMPT BIN
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
161 subj_bins = []
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
162 for bin in bins: #if we are not binning, bins = [] so for loop not entered
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
163 for acc in accs:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
164 if acc.split('.')[0] in bin.dict:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
165 try:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
166 queries[-1].bins[bin.label].append(len(queries[-1].matches))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
167 except:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
168 queries[-1].bins[bin.label] = [len(queries[-1].matches)]
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
169 subj_bins.append(bin.label)
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
170 break #this result has been binned to this bin so break
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
171 acc = accs[0]
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
172
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
173 score = int(float(cols[SCORE_COL]))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
174 p_cov = float(cols[PCOV_COL])
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
175
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
176 #SAVE RESULT
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
177 queries[-1].matches.append(BLASTMatch(acc, descr, score, p_cov, p_ident, subj_bins))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
178 output_tab.write(line)
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
179 input_tab.close()
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
180 output_tab.close()
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
181
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
182 '''
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
183 for query in queries:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
184 print(query)
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
185 for match in query.matches:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
186 print(' %s' % str(match))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
187 for bin in query.bins:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
188 print(' bin: %s' % bin)
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
189 for x in query.bins[bin]:
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
190 print(' %s' % str(query.matches[x]))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
191 '''
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
192
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
193 from Cheetah.Template import Template
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
194 namespace = {'queries': queries}
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
195 html = Template(file=cheetah_tmpl, searchList=[namespace])
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
196 out_html = open(output_html, 'w')
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
197 out_html.write(str(html))
18b097eb1a51 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 006cbba6513492f5a06b573c676400a2d464520b-dirty
dfornika
parents:
diff changeset
198 out_html.close()