blast2html: blast2html.py annotate

annotate blast2html.py @ 111:7aa28753d7b3

create document-wide h1 header, put other headers one size down

author	Jan Kanis <jan.code@jankanis.nl>
date	Wed, 09 Jul 2014 15:17:14 +0200
parents	e17aae23cc1c
children	0c2a03f9740b

rev	line source
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1 #!/usr/bin/env python3
50 bfc82a8aa3c9 unicodify python sources Jan Kanis <jan.code@jankanis.nl> parents: 27 diff changeset	2 # -- coding: utf-8 --
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	3
75 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	4 # Actually this program works with both python 2 and 3, tested against python 2.6
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	5
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	6 # Copyright The Hyve B.V. 2014
72 6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	7 # License: GPL version 3 or (at your option) any higher version
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	8
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	9 from __future__ import unicode_literals, division
50 bfc82a8aa3c9 unicodify python sources Jan Kanis <jan.code@jankanis.nl> parents: 27 diff changeset	10
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	11 import sys
7 9e7927673089 intermediate commit before converting some tables to divs Jan Kanis <jan.code@jankanis.nl> parents: 5 diff changeset	12 import math
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	13 import warnings
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	14 import six, codecs, io
75 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	15 from six.moves import builtins
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	16 from os import path
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	17 from itertools import repeat
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	18 from collections import defaultdict
99 8f02008a5f20 look at all blast.loc files; python2.6 compat fix Jan Kanis <jan.code@jankanis.nl>* parents: 98 diff changeset	19 import glob
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	20 import argparse
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	21 from lxml import objectify
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	22 import jinja2
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	23
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	24 builtin_str = str
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	25 str = six.text_type
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	26
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	27
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	28
76 7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	29 _filters = dict(float='float')
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	30 def filter(func_or_name):
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	31 "Decorator to register a function as filter in the current jinja environment"
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	32 if isinstance(func_or_name, six.string_types):
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	33 def inner(func):
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	34 _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	35 return func
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	36 return inner
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	37 else:
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	38 _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	39 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	40
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	41
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	42 def color_idx(length):
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	43 if length < 40:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	44 return 0
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	45 elif length < 50:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	46 return 1
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	47 elif length < 80:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	48 return 2
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	49 elif length < 200:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	50 return 3
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	51 return 4
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	52
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	53 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	54 def fmt(val, fmt):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	55 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	56
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	57 @filter
76 7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	58 def numfmt(val):
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	59 """Format numbers in decimal notation, but without excessive trailing 0's.
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	60 Default python float formatting will use scientific notation for some values,
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	61 or append trailing zeros with the 'f' format type, and the number of digits differs
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	62 between python 2 and 3."""
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	63 fpart, ipart = math.modf(val)
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	64 if fpart == 0:
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	65 return str(int(val))
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	66 # round to 10 to get identical representations in python 2 and 3
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	67 s = format(round(val, 10), '.10f').rstrip('0')
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	68 if s[-1] == '.':
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	69 s += '0'
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	70 return s
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	71
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	72 @filter
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	73 def firsttitle(hit):
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	74 return str(hit.Hit_def).split('>')[0]
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	75
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	76 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	77 def othertitles(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	78 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	79 id_titles = str(hit.Hit_def).split('>')
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 titles = []
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	82 for t in id_titles[1:]:
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	83 id, title = t.split(' ', 1)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	84 titles.append(argparse.Namespace(Hit_id = id,
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	85 Hit_def = title,
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	86 Hit_accession = '',
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	87 getroottree = hit.getroottree))
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	88 return titles
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	89
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	90 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	91 def hitid(hit):
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	92 return str(hit.Hit_id)
24 c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values Jan Kanis <jan.code@jankanis.nl> parents: 23 diff changeset	93
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	94
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	95 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	96 def alignment_pre(hsp):
68 fa8a93bdefd7 fix bug in calculations of alignment end Jan Kanis <jan.code@jankanis.nl> parents: 67 diff changeset	97 """Create the preformatted alignment blocks"""
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	98
371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	99 # line break length
371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	100 linewidth = 60
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	101
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	102 qfrom = int(hsp['Hsp_query-from'])
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	103 qto = int(hsp['Hsp_query-to'])
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	104 qframe = int(hsp['Hsp_query-frame'])
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	105 hfrom = int(hsp['Hsp_hit-from'])
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	106 hto = int(hsp['Hsp_hit-to'])
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	107 hframe = int(hsp['Hsp_hit-frame'])
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	108
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	109 qseq = hsp.Hsp_qseq.text
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	110 midline = hsp.Hsp_midline.text
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	111 hseq = hsp.Hsp_hseq.text
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	112
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	113 if not qframe in (1, -1):
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	114 warnings.warn("Error in BlastXML input: Hsp node {0} has a Hsp_query-frame of {1}. (should be 1 or -1)".format(nodeid(hsp), qframe))
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	115 qframe = -1 if qframe < 0 else 1
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	116 if not hframe in (1, -1):
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	117 warnings.warn("Error in BlastXML input: Hsp node {0} has a Hsp_hit-frame of {1}. (should be 1 or -1)".format(nodeid(hsp), hframe))
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	118 hframe = -1 if hframe < 0 else 1
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	119
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	120 def split(txt):
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	121 return [txt[i:i+linewidth] for i in range(0, len(txt), linewidth)]
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	122
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	123 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), linewidth)):
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	124 yield (
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	125 "Query {0:>7} {1} {2}\n".format(qfrom+offsetqframe, qs, qfrom+(offset+len(qs)-1)qframe) +
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	126 " {0:7} {1}\n".format('', mid) +
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	127 "Subject{0:>7} {1} {2}".format(hfrom+offsethframe, hs, hfrom+(offset+len(hs)-1)hframe)
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	128 )
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	129
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	130 if qfrom+(len(qseq)-1)*qframe != qto:
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	131 warnings.warn("Error in BlastXML input: Hsp node {0} qseq length mismatch: from {1} to {2} length {3}".format(
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	132 nodeid(hsp), qfrom, qto, len(qseq)))
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	133 if hfrom+(len(hseq)-1)*hframe != hto:
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	134 warnings.warn("Error in BlastXML input: Hsp node {0} hseq length mismatch: from {1} to {2} length {3}".format(
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	135 nodeid(hsp), hfrom, hto, len(hseq)))
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	136
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	137
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	138
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	139 @filter('len')
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	140 def blastxml_len(node):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	141 if node.tag == 'Hsp':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	142 return int(node['Hsp_align-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	143 elif node.tag == 'Iteration':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	144 return int(node['Iteration_query-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	145 raise Exception("Unknown XML node type: "+node.tag)
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	146
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	147 @filter
53 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	148 def nodeid(node):
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	149 id = []
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	150 if node.tag == 'Hsp':
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	151 id.insert(0, node.Hsp_num.text)
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	152 node = node.getparent().getparent()
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	153 assert node.tag == 'Hit'
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	154 if node.tag == 'Hit':
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	155 id.insert(0, node.Hit_num.text)
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	156 node = node.getparent().getparent()
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	157 assert node.tag == 'Iteration'
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	158 if node.tag == 'Iteration':
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	159 id.insert(0, node['Iteration_iter-num'].text)
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	160 return '-'.join(id)
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	161 raise ValueError("The nodeid filter can only be applied to Hsp, Hit or Iteration nodes in a BlastXML document")
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	162
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	163
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	164 @filter
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	165 def asframe(frame):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	166 if frame == 1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	167 return 'Plus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	168 elif frame == -1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	169 return 'Minus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	170 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	171
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	172 # def genelink(hit, type='genbank', hsp=None):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	173 # if not isinstance(hit, six.string_types):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	174 # hit = hitid(hit)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	175 # link = "http://www.ncbi.nlm.nih.gov/nucleotide/{0}?report={1}&log$=nuclalign".format(hit, type)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	176 # if hsp != None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	177 # link += "&from={0}&to={1}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	178 # return link
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	179
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	180
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	181 # 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	182 # 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	183
74 03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	184 # The r'\u0027' syntax doesn't work the way we need to in python 2.6 with unicode_literals
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	185 _base_js_escapes = (
74 03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	186 ('\\', '\\u005C'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	187 ('\'', '\\u0027'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	188 ('"', '\\u0022'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	189 # ('>', '\\u003E'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	190 # ('<', '\\u003C'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	191 # ('&', '\\u0026'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	192 # ('=', '\\u003D'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	193 # ('-', '\\u002D'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	194 # (';', '\\u003B'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	195 (u'\u2028', '\\u2028'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	196 (u'\u2029', '\\u2029')
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	197 )
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	198
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	199 # 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	200 # 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	201 # parsing mode.
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	202 _js_escapes = (_base_js_escapes +
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	203 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	204
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	205 @filter
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	206 def js_string_escape(value):
72 6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	207 """
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	208 Javascript string literal escape. Note that this only escapes data
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	209 for embedding within javascript string literals, not in general
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	210 javascript snippets.
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	211 """
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	212
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	213 value = str(value)
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	214
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	215 for bad, good in _js_escapes:
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	216 value = value.replace(bad, good)
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	217
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	218 return value
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	219
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	220 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	221 def hits(result):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	222 # sort hits by longest hotspot first
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	223 return sorted(result.Iteration_hits.findall('Hit'),
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	224 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	225 reverse=True)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	226
110 e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	227 @filter('params')
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	228 def result_params(iteration):
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	229 return (('Query number', iteration['Iteration_iter-num']),
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	230 ('Query ID', iteration['Iteration_query-ID']),
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	231 ('Definition line', iteration['Iteration_query-def']),
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	232 ('Length', blastxml_len(iteration)))
7 9e7927673089 intermediate commit before converting some tables to divs Jan Kanis <jan.code@jankanis.nl> parents: 5 diff changeset	233
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	234
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	235 class BlastVisualize:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	236
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	237 colors = ('black', 'blue', 'green', 'magenta', 'red')
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	238
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	239 max_scale_labels = 10
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	240
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	241 def __init__(self, input, templatedir, templatename, genelinks={}):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	242 self.input = input
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	243 self.templatename = templatename
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	244 self.genelinks = genelinks
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	245
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	246 self.blast = objectify.parse(self.input).getroot()
79 9fb1a7d67317 remove unneeded encoding parameter Jan Kanis <jan.code@jankanis.nl> parents: 78 diff changeset	247 self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	248 self.environment = jinja2.Environment(loader=self.loader,
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	249 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	250
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	251 self._addfilters(self.environment)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	252
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	253
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	254 def _addfilters(self, environment):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	255 for filtername, funcname in _filters.items():
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	256 try:
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	257 environment.filters[filtername] = getattr(self, funcname)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	258 except AttributeError:
75 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	259 try:
4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	260 environment.filters[filtername] = globals()[funcname]
4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	261 except KeyError:
4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	262 environment.filters[filtername] = getattr(builtins, funcname)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	263
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	264 def render(self, output):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	265 template = self.environment.get_template(self.templatename)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	266
110 e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	267 params = (('Program', self.blast.BlastOutput_version),
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	268 ('Database', self.blast.BlastOutput_db),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	269 )
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	270
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	271 result = template.stream(blast=self.blast,
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	272 iterations=self.blast.BlastOutput_iterations.Iteration,
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	273 colors=self.colors,
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	274 params=params)
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	275
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	276 result.dump(output)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	277
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	278 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	279 def match_colors(self, result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	280 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	281 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	282 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	283
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	284 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	285
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	286 percent_multiplier = 100 / query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	287
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	288 for hit in hits(result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	289 # 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	290 # 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	291 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	292 table = bytearray([255]) * query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	293 for hsp in hotspots:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	294 frm = hsp['Hsp_query-from'] - 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	295 to = int(hsp['Hsp_query-to'])
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	296 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	297
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	298 matches = []
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	299 last = table[0]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	300 count = 0
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	301 for i in range(query_length):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	302 if table[i] == last:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	303 count += 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	304 continue
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	305 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	306 last = table[i]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	307 count = 1
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	308 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	309
53 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	310 yield dict(colors=matches, hit=hit, defline=firsttitle(hit))
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	311
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	312 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	313 def queryscale(self, result):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	314 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	315 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	316 percent_multiplier = 100 / query_length
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	317 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	318 if i % skip == 0:
23 6995a6f34f3f fix sectioning, add footer Jan Kanis <jan.code@jankanis.nl> parents: 22 diff changeset	319 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	320 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	321 yield dict(label = query_length,
23 6995a6f34f3f fix sectioning, add footer Jan Kanis <jan.code@jankanis.nl> parents: 22 diff changeset	322 width = (query_length % skip) * percent_multiplier)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	323
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	324 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	325 def hit_info(self, result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	326
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	327 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	328
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	329 for hit in hits(result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	330 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	331
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	332 cover = [False] * query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	333 for hsp in hsps:
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	334 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	335 cover_count = cover.count(True)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	336
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	337 def hsp_val(path):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	338 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	339
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	340 yield dict(hit = hit,
75 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	341 title = firsttitle(hit),
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	342 maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))),
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	343 totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	344 cover = "{0:.0%}".format(cover_count / query_length),
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	345 e_value = "{0:.4g}".format(min(hsp_val('Hsp_evalue'))),
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	346 # FIXME: is this the correct formula vv?
78 c0804e6443c6 comment Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	347 # float(...) because non-flooring division doesn't work with lxml elements in python 2.6
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	348 ident = "{0:.0%}".format(float(min(float(hsp.Hsp_identity) / blastxml_len(hsp) for hsp in hsps))))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	349
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	350 @filter
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	351 def genelink(self, hit, text=None, clas=None, display_nolink=True):
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	352 """Create a html link from a hit node to a configured gene bank webpage.
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	353 text: The text of the link, defaults to the hit_id
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	354 clas: extra css classes that will be added to the <a> element
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	355 display_nolink: boolean, if false don't display anything if no link can be created. Default True.
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	356 """
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	357
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	358 if text is None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	359 text = hitid(hit)
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	360
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	361 db = hit.getroottree().getroot().BlastOutput_db
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	362
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	363 if isinstance(self.genelinks, six.string_types):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	364 template = self.genelinks
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	365 else:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	366 template = self.genelinks.get(db)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	367 if template is None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	368 return text if display_nolink else ''
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	369 args = dict(id=hitid(hit).split('\|'),
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	370 fullid=hitid(hit),
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	371 defline=str(hit.Hit_def).split(' ', 1)[0].split('\|'),
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	372 fulldefline=str(hit.Hit_def).split(' ', 1)[0],
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	373 accession=str(hit.Hit_accession))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	374 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	375 link = template.format(**args)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	376 except Exception as e:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	377 warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	378 return text if display_nolink else ''
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	379
99 8f02008a5f20 look at all blast.loc files; python2.6 compat fix Jan Kanis <jan.code@jankanis.nl>* parents: 98 diff changeset	380 classattr = 'class="{0}" '.format(jinja2.escape(clas)) if clas is not None else ''
8f02008a5f20 look at all blast.loc files; python2.6 compat fix Jan Kanis <jan.code@jankanis.nl>* parents: 98 diff changeset	381 return jinja2.Markup("<a {0}href=\"{1}\">{2}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text)))
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	382
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	383
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	384 def read_genelinks(dir):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	385 links = {}
99 8f02008a5f20 look at all blast.loc files; python2.6 compat fix Jan Kanis <jan.code@jankanis.nl>* parents: 98 diff changeset	386 # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc.
101 5bfaa3ee1f27 better warning message Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	387 files = sorted(glob.glob(path.join(dir, 'blastdb*.loc')))
5bfaa3ee1f27 better warning message Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	388 # reversed, so blastdb.loc will take precedence
5bfaa3ee1f27 better warning message Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	389 for f in reversed(files):
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	390 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	391 f = open(path.join(dir, f))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	392 for l in f.readlines():
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	393 if l.strip().startswith('#'):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	394 continue
98 e780606b7c25 test new command line parameters, fix small bug Jan Kanis <jan.code@jankanis.nl> parents: 96 diff changeset	395 line = l.rstrip('\n').split('\t')
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	396 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	397 links[line[2]] = line[3]
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	398 except IndexError:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	399 continue
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	400 f.close()
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	401 except OSError:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	402 continue
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	403 if not links:
103 86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	404 if not files:
86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	405 warnings.warn("No gene bank link templates found (no blastdb*.loc files found in {0})".format(dir))
86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	406 else:
86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	407 warnings.warn("No gene bank link templates found in {0}".format(', '.join(files)))
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	408 return links
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	409
27 4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy Jan Kanis <jan.code@jankanis.nl> parents: 24 diff changeset	410
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	411 def main():
27 4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy Jan Kanis <jan.code@jankanis.nl> parents: 24 diff changeset	412 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	413
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	414 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	415 usage="{0} [-i] INPUT [-o OUTPUT] [--genelink-template URL_TEMPLATE]".format(sys.argv[0]))
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	416 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	417 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	418 help='The input Blast XML file, same as -i/--input')
53 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	419 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'),
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	420 help='The input Blast XML file')
53 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	421 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	422 help='The output html file')
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	423 # 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	424 # 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	425 # 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	426 # 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	427 # care too much.
53 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	428 parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template,
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	429 help='The template file to use. Defaults to blast_html.html.jinja')
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	430
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	431 dblink_group = parser.add_mutually_exclusive_group()
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	432 dblink_group.add_argument('--genelink-template', metavar='URL_TEMPLATE',
b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	433 default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	434 help="""A link template to link hits to a gene bank webpage. The template string is a
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	435 Python format string. It can contain the following replacement elements: {id[N]}, {fullid},
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	436 {defline[N]}, {fulldefline}, {accession}, where N is a number. id[N] and defline[N] will be
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	437 replaced by the Nth element of the id or defline, where '\|' is the field separator.
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	438
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	439 The default is 'http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	440 which is a link to the NCBI nucleotide database.""")
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	441
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	442 dblink_group.add_argument('--db-config-dir',
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	443 help="""The directory where databases are configured in blastdb*.loc files. These files
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	444 are consulted for creating a gene bank link. The files should be tab-separated tables (with lines
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	445 starting with '#' ignored), where the third field of a line should be a database path and the fourth
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	446 a genebank link template conforming to the --genelink-template option syntax.
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	447
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	448 This option is incompatible with --genelink-template.""")
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	449
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	450 args = parser.parse_args()
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	451 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	452 args.input = args.positional_arg
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	453 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	454 parser.error('no input specified')
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	455
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	456 if six.PY2:
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	457 # The argparse.FileType wrapper doesn't support an encoding
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	458 # argument, so for python 2 we need to wrap or reopen the
b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	459 # output. The input files are already read as utf-8 by the
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	460 # respective libraries.
107 ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	461 #
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	462 # One option is using codecs, but the codecs' writelines()
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	463 # method doesn't support streaming but collects all output and
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	464 # writes at once (see Python issues #5445 and #21910). On the
b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	465 # other hand the io module is slower (though not
b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	466 # significantly).
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	467
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	468 # args.output = codecs.getwriter('utf-8')(args.output)
107 ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	469 # def fixed_writelines(iter, self=args.output):
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	470 # for i in iter:
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	471 # self.write(i)
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	472 # args.output.writelines = fixed_writelines
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	473
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	474 args.output.close()
109 ea3bc0b9a3d9 fix (again) output encoding Jan Kanis <jan.code@jankanis.nl> parents: 107 diff changeset	475 args.output = io.open(args.output.name, 'w', encoding='utf-8')
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	476
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	477 templatedir, templatename = path.split(args.template.name)
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	478 args.template.close()
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	479 if not templatedir:
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	480 templatedir = '.'
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	481
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	482 if args.db_config_dir is None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	483 genelinks = args.genelink_template
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	484 elif not path.isdir(args.db_config_dir):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	485 parser.error('db-config-dir does not exist or is not a directory')
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	486 else:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	487 genelinks = read_genelinks(args.db_config_dir)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	488
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	489 b = BlastVisualize(args.input, templatedir, templatename, genelinks)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	490 b.render(args.output)
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	491 args.output.close()
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	492
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	493
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	494 if __name__ == '__main__':
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	495 main()
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	496

Mercurial > repos > jankanis > blast2html

annotate blast2html.py @ 111:7aa28753d7b3