Mercurial > repos > jankanis > blast2html

annotate visualise.py @ 11:7660519f2dc9

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
proper layout for alignments, added some links
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 12 May 2014 13:55:04 +0200
parents 2fbdf2eb27b4
children a459c754cdb5
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
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
2
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
3 # Copyright The Hyve B.V. 2014
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
4 # License: GPL version 3 or higher
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
6 import sys
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
7 import math
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
8 import warnings
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
9 from itertools import repeat
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
10 from lxml import objectify
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
11 import jinja2
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
12
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
13
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
14 blast = objectify.parse('blast xml example1.xml').getroot()
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
15 loader = jinja2.FileSystemLoader(searchpath='.')
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
16 environment = jinja2.Environment(loader=loader, lstrip_blocks=True, trim_blocks=True, autoescape=True)
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
17
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
18 def filter(func_or_name):
11
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
19 "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
20 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
21 def inner(func):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
22 environment.filters[func_or_name] = func
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
23 return func
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
24 return inner
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
25 else:
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
26 environment.filters[func_or_name.__name__] = func_or_name
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
27 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
28
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
29
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
30 def color_idx(length):
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
31 if length < 40:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
32 return 0
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
33 elif length < 50:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
34 return 1
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
35 elif length < 80:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
36 return 2
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
37 elif length < 200:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
38 return 3
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
39 return 4
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
40
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
41 colors = ['black', 'blue', 'green', 'magenta', 'red']
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
42
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
43 environment.filters['color'] = lambda length: match_colors[color_idx(length)]
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
44
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
45 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
46 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
47 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
48
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
49 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
50 def firsttitle(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
51 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
52
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
53 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
54 def othertitles(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
55 """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
56 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
57
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
58 titles = []
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
59 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
60 fullid, title = t.split(' ', 1)
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
61 id = fullid.split('|', 2)[2]
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
62 titles.append(dict(id = id,
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
63 fullid = fullid,
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
64 title = title))
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
65 return titles
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
66
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
67 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
68 def hitid(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
69 return hit.Hit_id.text.split('|', 2)[1]
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
70
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
71 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
72 def seqid(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
73 return hit.Hit_id.text.split('|', 2)[2]
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
74
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
75 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
76 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
77 return (
11
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
78 "Query {:>7s} {} {}\n".format(hsp['Hsp_query-from'], hsp.Hsp_qseq, hsp['Hsp_query-to']) +
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
79 " {:7s} {}\n".format('', hsp.Hsp_midline) +
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
80 "Subject{:>7s} {} {}".format(hsp['Hsp_hit-from'], hsp.Hsp_hseq, hsp['Hsp_hit-to'])
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
81 )
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
82
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
83 @filter('len')
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
84 def hsplen(node):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
85 return int(node['Hsp_align-len'])
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
86
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
87 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
88 def asframe(frame):
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
89 if frame == 1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
90 return 'Plus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
91 elif frame == -1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
92 return 'Minus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
93 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
94
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
95
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
96 query_length = int(blast["BlastOutput_query-len"])
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
97
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
98 hits = blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
99 # sort hits by longest hotspot first
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
100 ordered_hits = sorted(hits,
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
101 key=lambda h: max(hsplen(hsp) for hsp in h.Hit_hsps.Hsp),
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
102 reverse=True)
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
103
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
104 def match_colors():
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
105 """
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
106 An iterator that yields lists of length-color pairs.
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
107 """
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
108
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
109 percent_multiplier = 100 / query_length
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
110
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
111 for hit in hits:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
112 # sort hotspots from short to long, so we can overwrite index colors of
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
113 # short matches with those of long ones.
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
114 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: hsplen(hsp))
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
115 table = bytearray([255]) * query_length
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
116 for hsp in hotspots:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
117 frm = hsp['Hsp_query-from'] - 1
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
118 to = int(hsp['Hsp_query-to'])
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
119 table[frm:to] = repeat(color_idx(hsplen(hsp)), to - frm)
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
120
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
121 matches = []
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
122 last = table[0]
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
123 count = 0
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
124 for i in range(query_length):
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
125 if table[i] == last:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
126 count += 1
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
127 continue
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
128 matches.append((count * percent_multiplier, colors[last] if last != 255 else 'none'))
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
129 last = table[i]
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
130 count = 1
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
131 matches.append((count * percent_multiplier, colors[last] if last != 255 else 'none'))
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
132
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
133 yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
134
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
135
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
136 def queryscale():
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
137 max_labels = 10
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
138 skip = math.ceil(query_length / max_labels)
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
139 percent_multiplier = 100 / query_length
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
140 for i in range(1, query_length+1):
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
141 if i % skip == 0:
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
142 yield dict(label = i, width = skip * percent_multiplier)
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
143 if query_length % skip != 0:
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
144 yield dict(label = query_length, width = (query_length % skip) * percent_multiplier)
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
145
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
146
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
147 def hit_info():
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
148
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
149 for hit in ordered_hits:
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
150 hsps = hit.Hit_hsps.Hsp
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
151
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
152 cover = [False] * query_length
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
153 for hsp in hsps:
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
154 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, hsplen(hsp))
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
155 cover_count = cover.count(True)
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
156
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
157 def hsp_val(path):
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
158 return (hsp[path] for hsp in hsps)
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
159
11
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
160 yield dict(hit = hit,
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
161 title = firsttitle(hit),
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
162 link_id = hit.Hit_num,
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
163 maxscore = "{:.1f}".format(float(max(hsp_val('Hsp_bit-score')))),
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
164 totalscore = "{:.1f}".format(float(sum(hsp_val('Hsp_bit-score')))),
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
165 cover = "{:.0%}".format(cover_count / query_length),
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
166 e_value = "{:.4g}".format(float(min(hsp_val('Hsp_evalue')))),
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
167 # FIXME: is this the correct formula vv?
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
168 ident = "{:.0%}".format(float(min(hsp.Hsp_identity / hsplen(hsp) for hsp in hsps))),
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
169 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
170
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
171
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
172 def main():
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
173 template = environment.get_template('visualise.html.jinja')
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
174
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
175 params = (('Query ID', blast["BlastOutput_query-ID"]),
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
176 ('Query definition', blast["BlastOutput_query-def"]),
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
177 ('Query length', blast["BlastOutput_query-len"]),
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
178 ('Program', blast.BlastOutput_version),
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
179 ('Database', blast.BlastOutput_db),
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
180 )
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
181
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
182 if len(blast.BlastOutput_iterations.Iteration) > 1:
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
183 warnings.warn("Multiple 'Iteration' elements found, showing only the first")
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
184
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
185 sys.stdout.write(template.render(blast=blast,
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
186 length=query_length,
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
187 hits=blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit,
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
188 colors=colors,
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
189 match_colors=match_colors(),
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
190 queryscale=queryscale(),
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
191 hit_info=hit_info(),
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
192 params=params))
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
193
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
194 main()
11
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
195
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
196 # http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
197 # http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
198
7660519f2dc9 proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
199 # http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nucltop&blast_rank=1&RID=PHWP1JNZ014