annotate blast2html.py @ 43:0d5d90291ce2

another attempt at getting dependencies right
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 20 May 2014 14:56:10 +0200
parents 4e6ac737ba17
children bfc82a8aa3c9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1 #!/usr/bin/env python3
27
4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
Jan Kanis <jan.code@jankanis.nl>
parents: 24
diff changeset
2 # Actually runs under either python 2 or 3
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
3
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
4 # Copyright The Hyve B.V. 2014
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
5 # License: GPL version 3 or higher
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
6
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
7 import sys
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
8 import math
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
9 import warnings
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
10 from os import path
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
11 from itertools import repeat
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
12 import argparse
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
13 from lxml import objectify
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
14 import jinja2
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
15
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
16
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
17
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
18 _filters = {}
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
19 def filter(func_or_name):
11
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
20 "Decorator to register a function as filter in the current jinja environment"
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
21 if isinstance(func_or_name, str):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
22 def inner(func):
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
23 _filters[func_or_name] = func.__name__
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
24 return func
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
25 return inner
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
26 else:
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
27 _filters[func_or_name.__name__] = func_or_name.__name__
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
28 return func_or_name
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
29
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
30
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
31 def color_idx(length):
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
32 if length < 40:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
33 return 0
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
34 elif length < 50:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
35 return 1
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
36 elif length < 80:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
37 return 2
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
38 elif length < 200:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
39 return 3
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
40 return 4
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
41
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
42 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
43 def fmt(val, fmt):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
44 return format(float(val), fmt)
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
45
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
46 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
47 def firsttitle(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
48 return hit.Hit_def.text.split('>')[0]
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
49
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
50 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
51 def othertitles(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
52 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
53 id_titles = hit.Hit_def.text.split('>')
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
54
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
55 titles = []
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
56 for t in id_titles[1:]:
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
57 fullid, title = t.split(' ', 1)
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
58 hitid, id = fullid.split('|', 2)[1:3]
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
59 titles.append(dict(id = id,
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
60 hitid = hitid,
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
61 fullid = fullid,
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
62 title = title))
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
63 return titles
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
64
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
65 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
66 def hitid(hit):
24
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
67 hitid = hit.Hit_id.text
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
68 s = hitid.split('|', 2)
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
69 if len(s) >= 2:
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
70 return s[1]
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
71 return hitid
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
72
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
73 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
74 def seqid(hit):
24
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
75 hitid = hit.Hit_id.text
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
76 s = hitid.split('|', 2)
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
77 if len(s) >= 3:
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
78 return s[2]
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
79 return hitid
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
80
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
81
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
82 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
83 def alignment_pre(hsp):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
84 return (
15
648b3b7437da minor update
Jan Kanis <jan.code@jankanis.nl>
parents: 14
diff changeset
85 "Query {:>7s} {} {}\n".format(hsp['Hsp_query-from'].text, hsp.Hsp_qseq, hsp['Hsp_query-to']) +
11
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
86 " {:7s} {}\n".format('', hsp.Hsp_midline) +
15
648b3b7437da minor update
Jan Kanis <jan.code@jankanis.nl>
parents: 14
diff changeset
87 "Subject{:>7s} {} {}".format(hsp['Hsp_hit-from'].text, hsp.Hsp_hseq, hsp['Hsp_hit-to'])
11
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
88 )
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
89
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
90 @filter('len')
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
91 def blastxml_len(node):
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
92 if node.tag == 'Hsp':
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
93 return int(node['Hsp_align-len'])
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
94 elif node.tag == 'Iteration':
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
95 return int(node['Iteration_query-len'])
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
96 raise Exception("Unknown XML node type: "+node.tag)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
97
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
98
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
99 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
100 def asframe(frame):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
101 if frame == 1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
102 return 'Plus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
103 elif frame == -1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
104 return 'Minus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
105 raise Exception("frame should be either +1 or -1")
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
106
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
107 def genelink(hit, type='genbank', hsp=None):
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
108 if not isinstance(hit, str):
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
109 hit = hitid(hit)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
110 link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
111 if hsp != None:
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
112 link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
16
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
113 return link
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
114
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
115
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
116 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
117 # I've removed the html escapes, since html escaping is already being performed by the template engine.
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
118
16
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
119 _base_js_escapes = (
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
120 ('\\', r'\u005C'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
121 ('\'', r'\u0027'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
122 ('"', r'\u0022'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
123 # ('>', r'\u003E'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
124 # ('<', r'\u003C'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
125 # ('&', r'\u0026'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
126 # ('=', r'\u003D'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
127 # ('-', r'\u002D'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
128 # (';', r'\u003B'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
129 # (u'\u2028', r'\u2028'),
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
130 # (u'\u2029', r'\u2029')
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
131 )
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
132
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
133 # Escape every ASCII character with a value less than 32. This is
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
134 # needed a.o. to prevent html parsers from jumping out of javascript
16
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
135 # parsing mode.
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
136 _js_escapes = (_base_js_escapes +
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
137 tuple(('%c' % z, '\\u%04X' % z) for z in range(32)))
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
138
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
139 @filter
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
140 def js_string_escape(value):
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
141 """Escape javascript string literal escapes. Note that this only works
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
142 within javascript string literals, not in general javascript
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
143 snippets."""
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
144
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
145 value = str(value)
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
146
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
147 for bad, good in _js_escapes:
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
148 value = value.replace(bad, good)
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
149
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
150 return value
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
151
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
152 @filter
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
153 def hits(result):
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
154 # sort hits by longest hotspot first
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
155 return sorted(result.Iteration_hits.findall('Hit'),
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
156 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp),
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
157 reverse=True)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
158
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
159
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
160
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
161 class BlastVisualize:
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
162
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
163 colors = ('black', 'blue', 'green', 'magenta', 'red')
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
164
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
165 max_scale_labels = 10
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
166
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
167 def __init__(self, input, templatedir, templatename):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
168 self.input = input
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
169 self.templatename = templatename
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
170
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
171 self.blast = objectify.parse(self.input).getroot()
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
172 self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
173 self.environment = jinja2.Environment(loader=self.loader,
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
174 lstrip_blocks=True, trim_blocks=True, autoescape=True)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
175
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
176 self._addfilters(self.environment)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
177
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
178
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
179 def _addfilters(self, environment):
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
180 for filtername, funcname in _filters.items():
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
181 try:
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
182 environment.filters[filtername] = getattr(self, funcname)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
183 except AttributeError:
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
184 environment.filters[filtername] = globals()[funcname]
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
185
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
186 def render(self, output):
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
187 template = self.environment.get_template(self.templatename)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
188
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
189 params = (('Query ID', self.blast["BlastOutput_query-ID"]),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
190 ('Query definition', self.blast["BlastOutput_query-def"]),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
191 ('Query length', self.blast["BlastOutput_query-len"]),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
192 ('Program', self.blast.BlastOutput_version),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
193 ('Database', self.blast.BlastOutput_db),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
194 )
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
195
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
196 output.write(template.render(blast=self.blast,
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
197 iterations=self.blast.BlastOutput_iterations.Iteration,
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
198 colors=self.colors,
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
199 # match_colors=self.match_colors(),
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
200 # hit_info=self.hit_info(),
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
201 genelink=genelink,
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
202 params=params))
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
203
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
204 @filter
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
205 def match_colors(self, result):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
206 """
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
207 An iterator that yields lists of length-color pairs.
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
208 """
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
209
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
210 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
211
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
212 percent_multiplier = 100 / query_length
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
213
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
214 for hit in hits(result):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
215 # sort hotspots from short to long, so we can overwrite index colors of
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
216 # short matches with those of long ones.
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
217 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp))
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
218 table = bytearray([255]) * query_length
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
219 for hsp in hotspots:
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
220 frm = hsp['Hsp_query-from'] - 1
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
221 to = int(hsp['Hsp_query-to'])
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
222 table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm)
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
223
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
224 matches = []
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
225 last = table[0]
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
226 count = 0
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
227 for i in range(query_length):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
228 if table[i] == last:
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
229 count += 1
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
230 continue
16
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
231 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
232 last = table[i]
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
233 count = 1
16
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
234 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
235
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
236 yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
237
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
238 @filter
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
239 def queryscale(self, result):
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
240 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
241 skip = math.ceil(query_length / self.max_scale_labels)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
242 percent_multiplier = 100 / query_length
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
243 for i in range(1, query_length+1):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
244 if i % skip == 0:
23
6995a6f34f3f fix sectioning, add footer
Jan Kanis <jan.code@jankanis.nl>
parents: 22
diff changeset
245 yield dict(label = i, width = skip * percent_multiplier)
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
246 if query_length % skip != 0:
20
53cd304c5f26 Add index for multiple results; fix layout of query ruler for edge case
Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
247 yield dict(label = query_length,
23
6995a6f34f3f fix sectioning, add footer
Jan Kanis <jan.code@jankanis.nl>
parents: 22
diff changeset
248 width = (query_length % skip) * percent_multiplier)
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
249
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
250 @filter
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
251 def hit_info(self, result):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
252
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
253 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
254
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
255 for hit in hits(result):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
256 hsps = hit.Hit_hsps.Hsp
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
257
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
258 cover = [False] * query_length
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
259 for hsp in hsps:
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
260 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp))
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
261 cover_count = cover.count(True)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
262
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
263 def hsp_val(path):
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
264 return (float(hsp[path]) for hsp in hsps)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
265
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
266 yield dict(hit = hit,
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
267 title = firsttitle(hit),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
268 link_id = hit.Hit_num,
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
269 maxscore = "{:.1f}".format(max(hsp_val('Hsp_bit-score'))),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
270 totalscore = "{:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
271 cover = "{:.0%}".format(cover_count / query_length),
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
272 e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
273 # FIXME: is this the correct formula vv?
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
274 ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))),
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
275 accession = hit.Hit_accession)
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
276
27
4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
Jan Kanis <jan.code@jankanis.nl>
parents: 24
diff changeset
277
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
278 def main():
27
4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
Jan Kanis <jan.code@jankanis.nl>
parents: 24
diff changeset
279 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')
4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
Jan Kanis <jan.code@jankanis.nl>
parents: 24
diff changeset
280
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
281 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
282 usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
283 input_group = parser.add_mutually_exclusive_group(required=True)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
284 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
285 help='The input Blast XML file, same as -i/--input')
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
286 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
287 help='The input Blast XML file')
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
288 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
289 help='The output html file')
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
290 # We just want the file name here, so jinja can open the file
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
291 # itself. But it is easier to just use a FileType so argparse can
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
292 # handle the errors. This introduces a small race condition when
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
293 # jinja later tries to re-open the template file, but we don't
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
294 # care too much.
27
4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
Jan Kanis <jan.code@jankanis.nl>
parents: 24
diff changeset
295 parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template,
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
296 help='The template file to use. Defaults to blast_html.html.jinja')
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
297
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
298 args = parser.parse_args()
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
299 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
300 args.input = args.positional_arg
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
301 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
302 parser.error('no input specified')
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
303
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
304 templatedir, templatename = path.split(args.template.name)
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
305 args.template.close()
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
306 if not templatedir:
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
307 templatedir = '.'
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
308
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
309 b = BlastVisualize(args.input, templatedir, templatename)
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
310 b.render(args.output)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
311
11
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
312
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
313 if __name__ == '__main__':
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
314 main()
11
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
315