blast2html: blast2html.py annotate

annotate blast2html.py @ 24:c8347745bbad

use Iteration_message tag; also work with unexpected Hit_id values

author	Jan Kanis <jan.code@jankanis.nl>
date	Thu, 15 May 2014 12:12:21 +0200
parents	6995a6f34f3f
children	4e6ac737ba17

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):
24 c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values Jan Kanis <jan.code@jankanis.nl> parents: 23 diff changeset	66 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	67 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	68 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	69 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	70 return hitid
10 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 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	74 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	75 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	76 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	77 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	78 return hitid
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values Jan Kanis <jan.code@jankanis.nl> parents: 23 diff changeset	79
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	80
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	81 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	82 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	83 return (
15 648b3b7437da minor update Jan Kanis <jan.code@jankanis.nl> parents: 14 diff changeset	84 "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	85 " {:7s} {}\n".format('', hsp.Hsp_midline) +
15 648b3b7437da minor update Jan Kanis <jan.code@jankanis.nl> parents: 14 diff changeset	86 "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	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('len')
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	90 def blastxml_len(node):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	91 if node.tag == 'Hsp':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	92 return int(node['Hsp_align-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	93 elif node.tag == 'Iteration':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	94 return int(node['Iteration_query-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	95 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	96
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	97
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	98 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	99 def asframe(frame):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	100 if frame == 1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	101 return 'Plus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	102 elif frame == -1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	103 return 'Minus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	104 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	105
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	106 def genelink(hit, type='genbank', hsp=None):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	107 if not isinstance(hit, str):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	108 hit = hitid(hit)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	109 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	110 if hsp != None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	111 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	112 return link
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	113
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	114
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	115 # 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	116 # 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	117
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	118 _base_js_escapes = (
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	119 ('\\', r'\u005C'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	120 ('\'', r'\u0027'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	121 ('"', r'\u0022'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	122 # ('>', r'\u003E'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	123 # ('<', r'\u003C'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	124 # ('&', r'\u0026'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	125 # ('=', r'\u003D'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	126 # ('-', r'\u002D'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	127 # (';', r'\u003B'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	128 # (u'\u2028', r'\u2028'),
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	129 # (u'\u2029', r'\u2029')
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	130 )
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	131
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	132 # 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	133 # 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	134 # parsing mode.
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	135 _js_escapes = (_base_js_escapes +
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	136 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	137
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	138 @filter
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	139 def js_string_escape(value):
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	140 """Escape javascript string literal escapes. Note that this only works
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	141 within javascript string literals, not in general javascript
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	142 snippets."""
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	143
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	144 value = str(value)
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	145
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	146 for bad, good in _js_escapes:
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	147 value = value.replace(bad, good)
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	148
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	149 return value
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	150
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	151 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	152 def hits(result):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	153 # sort hits by longest hotspot first
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	154 return sorted(result.Iteration_hits.findall('Hit'),
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	155 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	156 reverse=True)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	157
7 9e7927673089 intermediate commit before converting some tables to divs Jan Kanis <jan.code@jankanis.nl> parents: 5 diff changeset	158
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	159
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	160 class BlastVisualize:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	161
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	162 colors = ('black', 'blue', 'green', 'magenta', 'red')
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	163
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	164 max_scale_labels = 10
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	165
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	166 def __init__(self, input, templatedir, templatename):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	167 self.input = input
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	168 self.templatename = templatename
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	169
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	170 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	171 self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	172 self.environment = jinja2.Environment(loader=self.loader,
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	173 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	174
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	175 self._addfilters(self.environment)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	176
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	177
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	178 def _addfilters(self, environment):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	179 for filtername, funcname in _filters.items():
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	180 try:
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	181 environment.filters[filtername] = getattr(self, funcname)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	182 except AttributeError:
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	183 environment.filters[filtername] = globals()[funcname]
12 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 def render(self, output):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	186 template = self.environment.get_template(self.templatename)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	187
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	188 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	189 ('Query definition', self.blast["BlastOutput_query-def"]),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	190 ('Query length', self.blast["BlastOutput_query-len"]),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	191 ('Program', self.blast.BlastOutput_version),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	192 ('Database', self.blast.BlastOutput_db),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	193 )
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	194
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	195 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	196 iterations=self.blast.BlastOutput_iterations.Iteration,
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	197 colors=self.colors,
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	198 # match_colors=self.match_colors(),
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	199 # hit_info=self.hit_info(),
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	200 genelink=genelink,
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	201 params=params))
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	202
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	203 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	204 def match_colors(self, result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	205 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	206 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	207 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	208
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	209 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	210
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	211 percent_multiplier = 100 / query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	212
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	213 for hit in hits(result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	214 # 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	215 # 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	216 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	217 table = bytearray([255]) * query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	218 for hsp in hotspots:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	219 frm = hsp['Hsp_query-from'] - 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	220 to = int(hsp['Hsp_query-to'])
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	221 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	222
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	223 matches = []
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	224 last = table[0]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	225 count = 0
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	226 for i in range(query_length):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	227 if table[i] == last:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	228 count += 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	229 continue
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	230 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	231 last = table[i]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	232 count = 1
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	233 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	234
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	235 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	236
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	237 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	238 def queryscale(self, result):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	239 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	240 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	241 percent_multiplier = 100 / query_length
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	242 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	243 if i % skip == 0:
23 6995a6f34f3f fix sectioning, add footer Jan Kanis <jan.code@jankanis.nl> parents: 22 diff changeset	244 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	245 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	246 yield dict(label = query_length,
23 6995a6f34f3f fix sectioning, add footer Jan Kanis <jan.code@jankanis.nl> parents: 22 diff changeset	247 width = (query_length % skip) * percent_multiplier)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	248
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	249 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	250 def hit_info(self, result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	251
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	252 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	253
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	254 for hit in hits(result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	255 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	256
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	257 cover = [False] * query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	258 for hsp in hsps:
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	259 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	260 cover_count = cover.count(True)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	261
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	262 def hsp_val(path):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	263 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	264
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	265 yield dict(hit = hit,
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	266 title = firsttitle(hit),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	267 link_id = hit.Hit_num,
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	268 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	269 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	270 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	271 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	272 # 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	273 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	274 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	275
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	276 def main():
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	277
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	278 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	279 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	280 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	281 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	282 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	283 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	284 help='The input Blast XML file')
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	285 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	286 help='The output html file')
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	287 # 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	288 # 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	289 # 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	290 # 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	291 # care too much.
22 efce16c98650 rename blast2html Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	292 parser.add_argument('--template', type=argparse.FileType(mode='r'), default='blast2html.html.jinja',
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	293 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	294
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	295 args = parser.parse_args()
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	296 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	297 args.input = args.positional_arg
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	298 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	299 parser.error('no input specified')
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	300
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	301 templatedir, templatename = path.split(args.template.name)
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	302 args.template.close()
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	303 if not templatedir:
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	304 templatedir = '.'
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	305
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	306 b = BlastVisualize(args.input, templatedir, templatename)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	307 b.render(args.output)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	308
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	309
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	310 if __name__ == '__main__':
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	311 main()
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	312

Mercurial > repos > jankanis > blast2html

annotate blast2html.py @ 24:c8347745bbad