Mercurial > repos > jankanis > blast2html
annotate blast2html.py @ 74:03e044b5bcc2 py2.6
fix escaping of javascript literals
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Wed, 18 Jun 2014 16:58:25 +0200 |
| parents | 67b1a319c6dc |
| children | 4d2c25baf5a3 |
| 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 |
| 50 | 2 # -*- coding: utf-8 -*- |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
3 |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
4 # Actually this program works with both python 2 and 3 |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
5 |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
6 # Copyright The Hyve B.V. 2014 |
| 72 | 7 # License: GPL version 3 or (at your option) any higher version |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
8 |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
9 from __future__ import unicode_literals, division |
| 50 | 10 |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
11 import sys |
|
7
9e7927673089
intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents:
5
diff
changeset
|
12 import math |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
13 import warnings |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
14 import six, codecs |
|
18
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
15 from os import path |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
16 from itertools import repeat |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
17 import argparse |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
18 from lxml import objectify |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
19 import jinja2 |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
20 |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
21 |
|
10
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
22 |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
23 _filters = dict() |
|
10
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
24 def filter(func_or_name): |
|
11
7660519f2dc9
proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents:
10
diff
changeset
|
25 "Decorator to register a function as filter in the current jinja environment" |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
26 if isinstance(func_or_name, six.string_types): |
|
10
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
27 def inner(func): |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
28 _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
|
29 return func |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
30 return inner |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
31 else: |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
32 _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
|
33 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
|
34 |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
35 |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
36 def color_idx(length): |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
37 if length < 40: |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
38 return 0 |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
39 elif length < 50: |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
40 return 1 |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
41 elif length < 80: |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
42 return 2 |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
43 elif length < 200: |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
44 return 3 |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
45 return 4 |
|
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
46 |
|
10
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
47 @filter |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
48 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
|
49 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
|
50 |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
51 @filter |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
52 def firsttitle(hit): |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
53 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
|
54 |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
55 @filter |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
56 def othertitles(hit): |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
57 """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
|
58 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
|
59 |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
60 titles = [] |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
61 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
|
62 fullid, title = t.split(' ', 1) |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
63 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
|
64 titles.append(dict(id = id, |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
65 hitid = hitid, |
|
10
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
66 fullid = fullid, |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
67 title = title)) |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
68 return titles |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
69 |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
70 @filter |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
71 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
|
72 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
|
73 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
|
74 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
|
75 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
|
76 return hitid |
|
10
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
77 |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
78 @filter |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
79 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
|
80 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
|
81 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
|
82 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
|
83 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
|
84 return hitid |
|
c8347745bbad
use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents:
23
diff
changeset
|
85 |
|
10
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 alignment_pre(hsp): |
|
68
fa8a93bdefd7
fix bug in calculations of alignment end
Jan Kanis <jan.code@jankanis.nl>
parents:
67
diff
changeset
|
89 """Create the preformatted alignment blocks""" |
| 71 | 90 |
| 91 # line break length | |
| 92 linewidth = 60 | |
|
67
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
93 |
|
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
94 qfrom = int(hsp['Hsp_query-from']) |
|
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
95 qto = int(hsp['Hsp_query-to']) |
| 69 | 96 qframe = int(hsp['Hsp_query-frame']) |
|
67
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
97 hfrom = int(hsp['Hsp_hit-from']) |
|
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
98 hto = int(hsp['Hsp_hit-to']) |
| 69 | 99 hframe = int(hsp['Hsp_hit-frame']) |
| 71 | 100 |
|
67
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
101 qseq = hsp.Hsp_qseq.text |
|
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
102 midline = hsp.Hsp_midline.text |
|
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
103 hseq = hsp.Hsp_hseq.text |
| 69 | 104 |
| 71 | 105 if not qframe in (1, -1): |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
106 warnings.warn("Error in BlastXML input: Hsp node {0} has a Hsp_query-frame of {1}. (should be 1 or -1)".format(nodeid(hsp), qframe)) |
| 69 | 107 qframe = -1 if qframe < 0 else 1 |
| 71 | 108 if not hframe in (1, -1): |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
109 warnings.warn("Error in BlastXML input: Hsp node {0} has a Hsp_hit-frame of {1}. (should be 1 or -1)".format(nodeid(hsp), hframe)) |
| 69 | 110 hframe = -1 if hframe < 0 else 1 |
|
67
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
111 |
| 69 | 112 def split(txt): |
| 71 | 113 return [txt[i:i+linewidth] for i in range(0, len(txt), linewidth)] |
| 69 | 114 |
| 71 | 115 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), linewidth)): |
|
67
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
116 yield ( |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
117 "Query {0:>7} {1} {2}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) + |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
118 " {0:7} {1}\n".format('', mid) + |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
119 "Subject{0:>7} {1} {2}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe) |
|
67
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
120 ) |
|
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
121 |
| 69 | 122 if qfrom+(len(qseq)-1)*qframe != qto: |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
123 warnings.warn("Error in BlastXML input: Hsp node {0} qseq length mismatch: from {1} to {2} length {3}".format( |
|
67
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
124 nodeid(hsp), qfrom, qto, len(qseq))) |
| 69 | 125 if hfrom+(len(hseq)-1)*hframe != hto: |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
126 warnings.warn("Error in BlastXML input: Hsp node {0} hseq length mismatch: from {1} to {2} length {3}".format( |
|
67
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
127 nodeid(hsp), hfrom, hto, len(hseq))) |
|
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
128 |
|
19c48f2ec775
wrap alignments if they are too long
Jan Kanis <jan.code@jankanis.nl>
parents:
53
diff
changeset
|
129 |
|
10
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
130 |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
131 @filter('len') |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
132 def blastxml_len(node): |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
133 if node.tag == 'Hsp': |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
134 return int(node['Hsp_align-len']) |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
135 elif node.tag == 'Iteration': |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
136 return int(node['Iteration_query-len']) |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
137 raise Exception("Unknown XML node type: "+node.tag) |
|
10
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
138 |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
139 @filter |
|
53
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
140 def nodeid(node): |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
141 id = [] |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
142 if node.tag == 'Hsp': |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
143 id.insert(0, node.Hsp_num.text) |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
144 node = node.getparent().getparent() |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
145 assert node.tag == 'Hit' |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
146 if node.tag == 'Hit': |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
147 id.insert(0, node.Hit_num.text) |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
148 node = node.getparent().getparent() |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
149 assert node.tag == 'Iteration' |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
150 if node.tag == 'Iteration': |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
151 id.insert(0, node['Iteration_iter-num'].text) |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
152 return '-'.join(id) |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
153 raise ValueError("The nodeid filter can only be applied to Hsp, Hit or Iteration nodes in a BlastXML document") |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
154 |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
155 |
|
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
156 @filter |
|
10
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
157 def asframe(frame): |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
158 if frame == 1: |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
159 return 'Plus' |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
160 elif frame == -1: |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
161 return 'Minus' |
|
2fbdf2eb27b4
All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents:
7
diff
changeset
|
162 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
|
163 |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
164 def genelink(hit, type='genbank', hsp=None): |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
165 if not isinstance(hit, six.string_types): |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
166 hit = hitid(hit) |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
167 link = "http://www.ncbi.nlm.nih.gov/nucleotide/{0}?report={1}&log$=nuclalign".format(hit, type) |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
168 if hsp != None: |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
169 link += "&from={0}&to={1}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to']) |
| 16 | 170 return link |
| 171 | |
| 172 | |
| 173 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139 | |
| 174 # 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
|
175 |
|
74
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
176 # The r'\u0027' syntax doesn't work the way we need to in python 2.6 with unicode_literals |
| 16 | 177 _base_js_escapes = ( |
|
74
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
178 ('\\', '\\u005C'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
179 ('\'', '\\u0027'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
180 ('"', '\\u0022'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
181 # ('>', '\\u003E'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
182 # ('<', '\\u003C'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
183 # ('&', '\\u0026'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
184 # ('=', '\\u003D'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
185 # ('-', '\\u002D'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
186 # (';', '\\u003B'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
187 (u'\u2028', '\\u2028'), |
|
03e044b5bcc2
fix escaping of javascript literals
Jan Kanis <jan.code@jankanis.nl>
parents:
73
diff
changeset
|
188 (u'\u2029', '\\u2029') |
| 16 | 189 ) |
| 190 | |
| 191 # 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
|
192 # needed a.o. to prevent html parsers from jumping out of javascript |
| 16 | 193 # parsing mode. |
| 194 _js_escapes = (_base_js_escapes + | |
| 195 tuple(('%c' % z, '\\u%04X' % z) for z in range(32))) | |
| 196 | |
| 197 @filter | |
| 198 def js_string_escape(value): | |
| 72 | 199 """ |
| 200 Javascript string literal escape. Note that this only escapes data | |
| 201 for embedding within javascript string literals, not in general | |
| 202 javascript snippets. | |
| 203 """ | |
| 16 | 204 |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
205 value = six.text_type(value) |
| 16 | 206 |
| 207 for bad, good in _js_escapes: | |
| 208 value = value.replace(bad, good) | |
| 209 | |
| 210 return value | |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
211 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
212 @filter |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
213 def hits(result): |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
214 # sort hits by longest hotspot first |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
215 return sorted(result.Iteration_hits.findall('Hit'), |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
216 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
|
217 reverse=True) |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
218 |
|
7
9e7927673089
intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents:
5
diff
changeset
|
219 |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
220 |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
221 class BlastVisualize: |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
222 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
223 colors = ('black', 'blue', 'green', 'magenta', 'red') |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
224 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
225 max_scale_labels = 10 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
226 |
|
18
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
227 def __init__(self, input, templatedir, templatename): |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
228 self.input = input |
|
18
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
229 self.templatename = templatename |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
230 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
231 self.blast = objectify.parse(self.input).getroot() |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
232 self.loader = jinja2.FileSystemLoader(searchpath=templatedir, encoding='utf-8') |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
233 self.environment = jinja2.Environment(loader=self.loader, |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
234 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
|
235 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
236 self._addfilters(self.environment) |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
237 |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
238 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
239 def _addfilters(self, environment): |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
240 for filtername, funcname in _filters.items(): |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
241 try: |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
242 environment.filters[filtername] = getattr(self, funcname) |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
243 except AttributeError: |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
244 environment.filters[filtername] = globals()[funcname] |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
245 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
246 def render(self, output): |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
247 template = self.environment.get_template(self.templatename) |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
248 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
249 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
|
250 ('Query definition', self.blast["BlastOutput_query-def"]), |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
251 ('Query length', self.blast["BlastOutput_query-len"]), |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
252 ('Program', self.blast.BlastOutput_version), |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
253 ('Database', self.blast.BlastOutput_db), |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
254 ) |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
255 |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
256 result = template.render(blast=self.blast, |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
257 iterations=self.blast.BlastOutput_iterations.Iteration, |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
258 colors=self.colors, |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
259 # match_colors=self.match_colors(), |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
260 # hit_info=self.hit_info(), |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
261 genelink=genelink, |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
262 params=params) |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
263 if six.PY2: |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
264 result = result.encode('utf-8') |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
265 output.write(result) |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
266 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
267 @filter |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
268 def match_colors(self, result): |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
269 """ |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
270 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
|
271 """ |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
272 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
273 query_length = blastxml_len(result) |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
274 |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
275 percent_multiplier = 100 / query_length |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
276 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
277 for hit in hits(result): |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
278 # 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
|
279 # 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
|
280 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
|
281 table = bytearray([255]) * query_length |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
282 for hsp in hotspots: |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
283 frm = hsp['Hsp_query-from'] - 1 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
284 to = int(hsp['Hsp_query-to']) |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
285 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
|
286 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
287 matches = [] |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
288 last = table[0] |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
289 count = 0 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
290 for i in range(query_length): |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
291 if table[i] == last: |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
292 count += 1 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
293 continue |
| 16 | 294 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
|
295 last = table[i] |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
296 count = 1 |
| 16 | 297 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
|
298 |
|
53
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
299 yield dict(colors=matches, hit=hit, defline=firsttitle(hit)) |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
300 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
301 @filter |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
302 def queryscale(self, result): |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
303 query_length = blastxml_len(result) |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
304 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
|
305 percent_multiplier = 100 / query_length |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
306 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
|
307 if i % skip == 0: |
| 23 | 308 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
|
309 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
|
310 yield dict(label = query_length, |
| 23 | 311 width = (query_length % skip) * percent_multiplier) |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
312 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
313 @filter |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
314 def hit_info(self, result): |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
315 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
316 query_length = blastxml_len(result) |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
317 |
|
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
318 for hit in hits(result): |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
319 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
|
320 |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
321 cover = [False] * query_length |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
322 for hsp in hsps: |
|
19
67ddcb807b7d
make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents:
18
diff
changeset
|
323 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
|
324 cover_count = cover.count(True) |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
325 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
326 def hsp_val(path): |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
327 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
|
328 |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
329 yield dict(hit = hit, |
|
53
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
330 title = firsttitle(hit), |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
331 maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))), |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
332 totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))), |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
333 cover = "{0:.0%}".format(cover_count / query_length), |
|
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
334 e_value = "{0:.4g}".format(min(hsp_val('Hsp_evalue'))), |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
335 # FIXME: is this the correct formula vv? |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
336 ident = "{0:.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
|
337 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
|
338 |
|
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
|
339 |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
340 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
|
341 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja') |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
342 |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
343 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page", |
|
73
67b1a319c6dc
First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents:
72
diff
changeset
|
344 usage="{0} [-i] INPUT [-o OUTPUT]".format(sys.argv[0])) |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
345 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
|
346 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
|
347 help='The input Blast XML file, same as -i/--input') |
|
53
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
348 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
349 help='The input Blast XML file') |
|
53
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
350 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout, |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
351 help='The output html file') |
|
18
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
352 # 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
|
353 # 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
|
354 # 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
|
355 # 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
|
356 # care too much. |
|
53
4217bb9cf1d3
depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents:
51
diff
changeset
|
357 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
|
358 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
|
359 |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
360 args = parser.parse_args() |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
361 if args.input == None: |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
362 args.input = args.positional_arg |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
363 if args.input == None: |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
364 parser.error('no input specified') |
|
5
1df2bfce5c24
first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
365 |
|
18
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
366 templatedir, templatename = path.split(args.template.name) |
|
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
367 args.template.close() |
|
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
368 if not templatedir: |
|
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
369 templatedir = '.' |
|
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
370 |
|
4434ffab721a
add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents:
16
diff
changeset
|
371 b = BlastVisualize(args.input, templatedir, templatename) |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
372 b.render(args.output) |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
373 |
|
11
7660519f2dc9
proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents:
10
diff
changeset
|
374 |
|
12
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
375 if __name__ == '__main__': |
|
a459c754cdb5
add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents:
11
diff
changeset
|
376 main() |
|
11
7660519f2dc9
proper layout for alignments, added some links
Jan Kanis <jan.code@jankanis.nl>
parents:
10
diff
changeset
|
377 |