blast2html: blast2html.py annotate

annotate blast2html.py @ 41:3173dfa849cc draft

update dependency

author	Jan Kanis <jan.code@jankanis.nl>
date	Mon, 19 May 2014 15:09:55 +0200
parents	4e6ac737ba17
children	bfc82a8aa3c9

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

Mercurial > repos > jankanis > blast2html

annotate blast2html.py @ 41:3173dfa849cc draft