blast2html: blast_html.py annotate

annotate blast_html.py @ 20:53cd304c5f26

Add index for multiple results; fix layout of query ruler for edge case The query ruler did not layout nicely if the last segment was too short to contain the text. For very short last segments the text is now displayed after the ruler.

author	Jan Kanis <jan.code@jankanis.nl>
date	Wed, 14 May 2014 16:20:29 +0200
parents	67ddcb807b7d
children

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
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	9 from os import path
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	10 from itertools import repeat
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	11 import argparse
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	12 from lxml import objectify
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	13 import jinja2
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	14
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	15
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	16
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	17 _filters = {}
10 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):
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	22 _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	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:
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	26 _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	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
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	41 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	42 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	43 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	44
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 firsttitle(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	47 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	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 othertitles(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	51 """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	52 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	53
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	54 titles = []
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	55 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	56 fullid, title = t.split(' ', 1)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	57 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	58 titles.append(dict(id = id,
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	59 hitid = hitid,
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	60 fullid = fullid,
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	61 title = title))
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	62 return titles
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	63
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	64 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	65 def hitid(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	66 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	67
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	68 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	69 def seqid(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	70 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	71
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	72 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	73 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	74 return (
15 648b3b7437da minor update Jan Kanis <jan.code@jankanis.nl> parents: 14 diff changeset	75 "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	76 " {:7s} {}\n".format('', hsp.Hsp_midline) +
15 648b3b7437da minor update Jan Kanis <jan.code@jankanis.nl> parents: 14 diff changeset	77 "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	78 )
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	79
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	80 @filter('len')
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	81 def blastxml_len(node):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	82 if node.tag == 'Hsp':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	83 return int(node['Hsp_align-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	84 elif node.tag == 'Iteration':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	85 return int(node['Iteration_query-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	86 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	87
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	88
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	89 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	90 def asframe(frame):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	91 if 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 'Plus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	93 elif frame == -1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	94 return 'Minus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	95 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	96
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	97 def genelink(hit, type='genbank', hsp=None):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	98 if not isinstance(hit, str):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	99 hit = hitid(hit)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	100 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	101 if hsp != None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	102 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	103 return link
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	104
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	105
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	106 # 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	107 # 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	108
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	109 _base_js_escapes = (
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	110 ('\\', r'\u005C'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	111 ('\'', r'\u0027'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	112 ('"', r'\u0022'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	113 # ('>', r'\u003E'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	114 # ('<', r'\u003C'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	115 # ('&', r'\u0026'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	116 # ('=', r'\u003D'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	117 # ('-', r'\u002D'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	118 # (';', r'\u003B'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	119 # (u'\u2028', r'\u2028'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	120 # (u'\u2029', r'\u2029')
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	121 )
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	122
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	123 # 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	124 # 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	125 # parsing mode.
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	126 _js_escapes = (_base_js_escapes +
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	127 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	128
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	129 @filter
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	130 def js_string_escape(value):
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	131 """Escape javascript string literal escapes. Note that this only works
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	132 within javascript string literals, not in general javascript
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	133 snippets."""
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	134
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	135 value = str(value)
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	136
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	137 for bad, good in _js_escapes:
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	138 value = value.replace(bad, good)
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	139
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	140 return value
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	141
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	142 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	143 def hits(result):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	144 # sort hits by longest hotspot first
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	145 return sorted(result.Iteration_hits.findall('Hit'),
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	146 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	147 reverse=True)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	148
7 9e7927673089 intermediate commit before converting some tables to divs Jan Kanis <jan.code@jankanis.nl> parents: 5 diff changeset	149
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	150
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	151 class BlastVisualize:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	152
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	153 colors = ('black', 'blue', 'green', 'magenta', 'red')
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	154
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	155 max_scale_labels = 10
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	156
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	157 def __init__(self, input, templatedir, templatename):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	158 self.input = input
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	159 self.templatename = templatename
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	160
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	161 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	162 self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	163 self.environment = jinja2.Environment(loader=self.loader,
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	164 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	165
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	166 self._addfilters(self.environment)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	167
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	168
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	169 def _addfilters(self, environment):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	170 for filtername, funcname in _filters.items():
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	171 try:
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	172 environment.filters[filtername] = getattr(self, funcname)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	173 except AttributeError:
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	174 environment.filters[filtername] = globals()[funcname]
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	175
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	176 def render(self, output):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	177 template = self.environment.get_template(self.templatename)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	178
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	179 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	180 ('Query definition', self.blast["BlastOutput_query-def"]),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	181 ('Query length', self.blast["BlastOutput_query-len"]),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	182 ('Program', self.blast.BlastOutput_version),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	183 ('Database', self.blast.BlastOutput_db),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	184 )
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 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	187 iterations=self.blast.BlastOutput_iterations.Iteration,
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	188 colors=self.colors,
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	189 # match_colors=self.match_colors(),
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	190 # hit_info=self.hit_info(),
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	191 genelink=genelink,
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	192 params=params))
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	193
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	194 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	195 def match_colors(self, result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	196 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	197 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	198 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	199
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	200 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	201
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	202 percent_multiplier = 100 / query_length
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 for hit in hits(result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	205 # 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	206 # 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	207 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	208 table = bytearray([255]) * query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	209 for hsp in hotspots:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	210 frm = hsp['Hsp_query-from'] - 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	211 to = int(hsp['Hsp_query-to'])
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	212 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	213
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	214 matches = []
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	215 last = table[0]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	216 count = 0
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	217 for i in range(query_length):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	218 if table[i] == last:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	219 count += 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	220 continue
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	221 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	222 last = table[i]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	223 count = 1
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	224 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	225
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	226 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	227
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	228 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	229 def queryscale(self, result):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	230 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	231 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	232 percent_multiplier = 100 / query_length
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	233 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	234 if i % 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	235 yield dict(label = i, width = skip * percent_multiplier, shorter = False)
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	236 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	237 yield dict(label = query_length,
53cd304c5f26 Add index for multiple results; fix layout of query ruler for edge case Jan Kanis <jan.code@jankanis.nl> parents: 19 diff changeset	238 width = (query_length % skip) * percent_multiplier,
53cd304c5f26 Add index for multiple results; fix layout of query ruler for edge case Jan Kanis <jan.code@jankanis.nl> parents: 19 diff changeset	239 shorter = True)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	240
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	241 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	242 def hit_info(self, result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	243
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	244 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	245
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	246 for hit in hits(result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	247 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	248
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	249 cover = [False] * query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	250 for hsp in hsps:
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	251 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	252 cover_count = cover.count(True)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	253
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	254 def hsp_val(path):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	255 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	256
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	257 yield dict(hit = hit,
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	258 title = firsttitle(hit),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	259 link_id = hit.Hit_num,
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	260 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	261 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	262 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	263 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	264 # 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	265 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	266 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	267
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	268 def main():
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	269
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	270 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	271 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	272 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	273 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	274 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	275 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	276 help='The input Blast XML file')
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	277 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	278 help='The output html file')
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	279 # 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	280 # 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	281 # 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	282 # 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	283 # care too much.
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	284 parser.add_argument('--template', type=argparse.FileType(mode='r'), default='blast_html.html.jinja',
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	285 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	286
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	287 args = parser.parse_args()
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	288 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	289 args.input = args.positional_arg
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	290 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	291 parser.error('no input specified')
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	292
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	293 templatedir, templatename = path.split(args.template.name)
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	294 args.template.close()
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	295 if not templatedir:
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	296 templatedir = '.'
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	297
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	298 b = BlastVisualize(args.input, templatedir, templatename)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	299 b.render(args.output)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	300
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	301
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	302 if __name__ == '__main__':
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	303 main()
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	304

Mercurial > repos > jankanis > blast2html

annotate blast_html.py @ 20:53cd304c5f26