blast2html: blast2html.py annotate

annotate blast2html.py @ 120:2729c2326235

Fix for Rikilt issue 13 Hit e-value and identity% should be taken from the hsp with the highest bit score. Previously each of these values was calculated independently. Also use arrays for cover calculation instead of python lists and refactor the hit_info() code a bit.

author	Jan Kanis <jan.code@jankanis.nl>
date	Thu, 31 Jul 2014 16:14:36 +0200
parents	591dc9c24824
children	5f104d05aa23

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
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	18 from collections import defaultdict, namedtuple
120 2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	19 from array import array
99 8f02008a5f20 look at all blast.loc files; python2.6 compat fix Jan Kanis <jan.code@jankanis.nl>* parents: 98 diff changeset	20 import glob
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	21 import argparse
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	22 from lxml import objectify
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	23 import jinja2
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	24
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	25 builtin_str = str
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	26 str = six.text_type
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	27
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	28
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	29
76 7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	30 _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	31 def filter(func_or_name):
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	32 "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	33 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	34 def inner(func):
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	35 _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	36 return func
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	37 return inner
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	38 else:
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	39 _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	40 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	41
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	42
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	43 def color_idx(length):
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	44 if length < 40:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	45 return 0
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	46 elif length < 50:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	47 return 1
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	48 elif length < 80:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	49 return 2
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	50 elif length < 200:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	51 return 3
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	52 return 4
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	53
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	54 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	55 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	56 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	57
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	58 @filter
76 7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	59 def numfmt(val):
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	60 """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	61 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	62 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	63 between python 2 and 3."""
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	64 fpart, ipart = math.modf(val)
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	65 if fpart == 0:
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	66 return str(int(val))
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	67 # 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	68 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	69 if s[-1] == '.':
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	70 s += '0'
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	71 return s
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	72
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	73 @filter
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	74 def firsttitle(hit):
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	75 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	76
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	77 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	78 def othertitles(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	79 """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	80 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	81
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	82 titles = []
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	83 for t in id_titles[1:]:
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	84 id, title = t.split(' ', 1)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	85 titles.append(argparse.Namespace(Hit_id = id,
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	86 Hit_def = title,
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	87 Hit_accession = '',
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	88 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	89 return titles
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	90
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	91 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	92 def hitid(hit):
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	93 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	94
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	95
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	96 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	97 def alignment_pre(hsp):
68 fa8a93bdefd7 fix bug in calculations of alignment end Jan Kanis <jan.code@jankanis.nl> parents: 67 diff changeset	98 """Create the preformatted alignment blocks"""
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	99
371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	100 # line break length
371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	101 linewidth = 60
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	102
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	103 qfrom = int(hsp['Hsp_query-from'])
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	104 qto = int(hsp['Hsp_query-to'])
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	105 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	106 hfrom = int(hsp['Hsp_hit-from'])
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	107 hto = int(hsp['Hsp_hit-to'])
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	108 hframe = int(hsp['Hsp_hit-frame'])
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	109
67 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	110 qseq = hsp.Hsp_qseq.text
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	111 midline = hsp.Hsp_midline.text
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	112 hseq = hsp.Hsp_hseq.text
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	113
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	114 if not qframe in (1, -1):
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	115 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	116 qframe = -1 if qframe < 0 else 1
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	117 if not hframe in (1, -1):
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	118 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	119 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	120
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	121 def split(txt):
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	122 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	123
71 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	124 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	125 yield (
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	126 "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	127 " {0:7} {1}\n".format('', mid) +
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	128 "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	129 )
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	130
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	131 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	132 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	133 nodeid(hsp), qfrom, qto, len(qseq)))
69 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 68 diff changeset	134 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	135 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	136 nodeid(hsp), hfrom, hto, len(hseq)))
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	137
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	138
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	139
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	140 @filter('len')
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	141 def blastxml_len(node):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	142 if node.tag == 'Hsp':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	143 return int(node['Hsp_align-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	144 elif node.tag == 'Iteration':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	145 return int(node['Iteration_query-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	146 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	147
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	148 @filter
53 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	149 def nodeid(node):
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	150 id = []
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	151 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	152 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	153 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	154 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	155 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	156 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	157 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	158 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	159 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	160 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	161 return '-'.join(id)
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	162 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	163
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	164
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	165 @filter
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	166 def asframe(frame):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	167 if frame == 1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	168 return 'Plus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	169 elif frame == -1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	170 return 'Minus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	171 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	172
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	173 # def genelink(hit, type='genbank', hsp=None):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	174 # if not isinstance(hit, six.string_types):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	175 # hit = hitid(hit)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	176 # 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	177 # if hsp != None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	178 # 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	179 # return link
16 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
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	182 # 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	183 # 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	184
74 03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	185 # 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	186 _base_js_escapes = (
74 03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	187 ('\\', '\\u005C'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	188 ('\'', '\\u0027'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	189 ('"', '\\u0022'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	190 # ('>', '\\u003E'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	191 # ('<', '\\u003C'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	192 # ('&', '\\u0026'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	193 # ('=', '\\u003D'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	194 # ('-', '\\u002D'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	195 # (';', '\\u003B'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	196 (u'\u2028', '\\u2028'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	197 (u'\u2029', '\\u2029')
16 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
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	200 # 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	201 # 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	202 # parsing mode.
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	203 _js_escapes = (_base_js_escapes +
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	204 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	205
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	206 @filter
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	207 def js_string_escape(value):
72 6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	208 """
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	209 Javascript string literal escape. Note that this only escapes data
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	210 for embedding within javascript string literals, not in general
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	211 javascript snippets.
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	212 """
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	213
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	214 value = str(value)
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	215
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	216 for bad, good in _js_escapes:
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	217 value = value.replace(bad, good)
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	218
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	219 return value
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	220
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	221 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	222 def hits(result):
119 591dc9c24824 tentative fix for Rikilt issue 10: don't sort hits ourselves but use blastxml ordering Jan Kanis <jan.code@jankanis.nl> parents: 118 diff changeset	223 # Use findall so we get an empty list if there are no Hit elements at all
591dc9c24824 tentative fix for Rikilt issue 10: don't sort hits ourselves but use blastxml ordering Jan Kanis <jan.code@jankanis.nl> parents: 118 diff changeset	224 return result.Iteration_hits.findall('Hit')
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	225
110 e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	226 @filter('params')
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	227 def result_params(iteration):
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	228 return (('Query number', iteration['Iteration_iter-num']),
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	229 ('Query ID', iteration['Iteration_query-ID']),
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	230 ('Definition line', iteration['Iteration_query-def']),
e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	231 ('Length', blastxml_len(iteration)))
7 9e7927673089 intermediate commit before converting some tables to divs Jan Kanis <jan.code@jankanis.nl> parents: 5 diff changeset	232
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	233
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	234 class BlastVisualize:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	235
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	236 colors = ('black', 'blue', 'green', 'magenta', 'red')
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	237
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	238 max_scale_labels = 10
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	239
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	240 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	241 self.input = input
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	242 self.templatename = templatename
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	243 self.genelinks = genelinks
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	244
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	245 self.blast = objectify.parse(self.input).getroot()
79 9fb1a7d67317 remove unneeded encoding parameter Jan Kanis <jan.code@jankanis.nl> parents: 78 diff changeset	246 self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	247 self.environment = jinja2.Environment(loader=self.loader,
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	248 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	249
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	250 self._addfilters(self.environment)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	251
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	252
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	253 def _addfilters(self, environment):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	254 for filtername, funcname in _filters.items():
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	255 try:
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	256 environment.filters[filtername] = getattr(self, funcname)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	257 except AttributeError:
75 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	258 try:
4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	259 environment.filters[filtername] = globals()[funcname]
4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	260 except KeyError:
4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	261 environment.filters[filtername] = getattr(builtins, funcname)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	262
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	263 def render(self, output):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	264 template = self.environment.get_template(self.templatename)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	265
110 e17aae23cc1c report query parameters for each query Jan Kanis <jan.code@jankanis.nl> parents: 109 diff changeset	266 params = (('Program', self.blast.BlastOutput_version),
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	267 ('Database', self.blast.BlastOutput_db),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	268 )
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	269
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	270 result = template.stream(blast=self.blast,
73 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	271 iterations=self.blast.BlastOutput_iterations.Iteration,
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	272 colors=self.colors,
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 72 diff changeset	273 params=params)
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	274
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	275 result.dump(output)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	276
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	277 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	278 def match_colors(self, result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	279 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	280 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	281 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	282
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	283 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	284
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	285 percent_multiplier = 100 / query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	286
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	287 for hit in hits(result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	288 # 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	289 # 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	290 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	291 table = bytearray([255]) * query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	292 for hsp in hotspots:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	293 frm = hsp['Hsp_query-from'] - 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	294 to = int(hsp['Hsp_query-to'])
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	295 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	296
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	297 matches = []
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	298 last = table[0]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	299 count = 0
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	300 for i in range(query_length):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	301 if table[i] == last:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	302 count += 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	303 continue
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	304 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	305 last = table[i]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	306 count = 1
16 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 15 diff changeset	307 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	308
53 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 51 diff changeset	309 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	310
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	311 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	312 def queryscale(self, result):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	313 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	314 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	315 percent_multiplier = 100 / query_length
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	316 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	317 if i % skip == 0:
23 6995a6f34f3f fix sectioning, add footer Jan Kanis <jan.code@jankanis.nl> parents: 22 diff changeset	318 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	319 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	320 yield dict(label = query_length,
23 6995a6f34f3f fix sectioning, add footer Jan Kanis <jan.code@jankanis.nl> parents: 22 diff changeset	321 width = (query_length % skip) * percent_multiplier)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	322
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	323 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	324 def hit_info(self, result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	325
19 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	326 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	327
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	328 for hit in hits(result):
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	329 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	330
120 2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	331 cover = array('B', [0]) * query_length
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	332 for hsp in hsps:
120 2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	333 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = array('B', [1]) * blastxml_len(hsp)
2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	334 cover_count = cover.count(1)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	335
120 2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	336 best_hsp = max(hsps, key=lambda h: h['Hsp_bit-score'])
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	337
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	338 yield dict(hit = hit,
75 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	339 title = firsttitle(hit),
120 2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	340 maxscore = format(float(best_hsp['Hsp_bit-score']), '.1f'),
2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	341 e_value = format(float(best_hsp.Hsp_evalue), '.4'),
78 c0804e6443c6 comment Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	342 # float(...) because non-flooring division doesn't work with lxml elements in python 2.6
120 2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	343 ident = format(float(best_hsp.Hsp_identity) / blastxml_len(best_hsp), '.0%'),
2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	344 totalscore = format(sum(hsp['Hsp_bit-score'] for hsp in hsps), '.1f'),
2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	345 cover = format(cover_count / query_length, '.0%'),
2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	346 )
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	347
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	348 @filter
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	349 def genelink(self, hit, text=None, text_from='hitid', cssclass=None, display_nolink=True):
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	350 """Create a html link from a hit node to a configured gene bank webpage.
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	351 text: The text of the link. If not set applies text_from.
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	352 text_from: string, if text is not specified, take it from specified source. Either 'hitid' (default) or 'dbname'.
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	353 cssclass: extra css classes that will be added to the <a> element
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	354 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	355 """
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	356
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	357 db = hit.getroottree().getroot().BlastOutput_db
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	358
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	359 template = self.genelinks[db].template
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	360
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	361 if text is None:
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	362 if text_from == 'hitid':
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	363 text = hitid(hit)
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	364 elif text_from == 'dbname':
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	365 text = self.genelinks[db].dbname
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	366 else:
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	367 raise ValueError("Unknown value for text_from: '{0}'. Use 'hitid' or 'dbname'.".format(text_from))
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	368
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	369 if template is None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	370 return text if display_nolink else ''
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	371
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	372 args = dict(id=hitid(hit).split('\|'),
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	373 fullid=hitid(hit),
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	374 defline=str(hit.Hit_def).split(' ', 1)[0].split('\|'),
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	375 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	376 accession=str(hit.Hit_accession))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	377 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	378 link = template.format(**args)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	379 except Exception as e:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	380 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	381 return text if display_nolink else ''
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	382
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	383 classattr = 'class="{0}" '.format(jinja2.escape(cssclass)) if cssclass is not None else ''
118 7f3f8c10f44b fix for Rikilt issues 8, 11, 12, 14 Jan Kanis <jan.code@jankanis.nl> parents: 116 diff changeset	384 return jinja2.Markup("<a {0}target=\"_top\" 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	385
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	386
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	387 genelinks_entry = namedtuple('genelinks_entry', 'dbname template')
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	388 def read_blastdb(dir, default):
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	389 links = defaultdict(lambda: default)
99 8f02008a5f20 look at all blast.loc files; python2.6 compat fix Jan Kanis <jan.code@jankanis.nl>* parents: 98 diff changeset	390 # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc.
101 5bfaa3ee1f27 better warning message Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	391 files = sorted(glob.glob(path.join(dir, 'blastdb*.loc')))
5bfaa3ee1f27 better warning message Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	392 # reversed, so blastdb.loc will take precedence
5bfaa3ee1f27 better warning message Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	393 for f in reversed(files):
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	394 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	395 f = open(path.join(dir, f))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	396 for l in f.readlines():
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	397 if l.strip().startswith('#'):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	398 continue
98 e780606b7c25 test new command line parameters, fix small bug Jan Kanis <jan.code@jankanis.nl> parents: 96 diff changeset	399 line = l.rstrip('\n').split('\t')
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	400 try:
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	401 links[line[2]] = genelinks_entry(dbname=line[3] or default.dbname, template=line[4])
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	402 except IndexError:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	403 continue
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	404 f.close()
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	405 except OSError:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	406 continue
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	407 if not links:
103 86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	408 if not files:
86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	409 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	410 else:
86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	411 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	412 return links
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	413
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	414
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	415 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	416 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	417
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	418 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	419 usage="{0} [-i] INPUT [-o OUTPUT] [--genelink-template URL_TEMPLATE] [--dbname DBNAME]".format(sys.argv[0]))
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	420 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	421 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	422 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	423 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	424 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	425 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	426 help='The output html file')
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	427 # 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	428 # 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	429 # 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	430 # 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	431 # 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	432 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	433 help='The template file to use. Defaults to blast_html.html.jinja')
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	434
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	435 parser.add_argument('--dbname', type=str, default='Gene Bank',
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	436 help="The link text to use for external links to a gene bank database. Defaults to 'Gene Bank'")
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	437 parser.add_argument('--genelink-template', metavar='URL_TEMPLATE',
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	438 default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	439 help="""A link template to link hits to a gene bank webpage. The template string is a
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	440 Python format string. It can contain the following replacement elements: {id[N]}, {fullid},
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	441 {defline[N]}, {fulldefline}, {accession}, where N is a number. id[N] and defline[N] will be
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	442 replaced by the Nth element of the id or defline, where '\|' is the field separator.
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	443
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	444 The default is 'http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	445 which is a link to the NCBI nucleotide database.""")
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	446
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	447 parser.add_argument('--db-config-dir',
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	448 help="""The directory where databases are configured in blastdb*.loc files. These files
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	449 are consulted for creating a gene bank link. The files should conform to the format that
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	450 Galaxy's BLAST expect, i.e. tab-separated tables (with lines starting with '#' ignored),
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	451 with two extra fields. The third field of a line should be a database path and the fourth
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	452 a genebank link template conforming to the --genelink-template option syntax. Entries in
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	453 these config files override links specified using --genelink-template and --dbname.""")
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	454
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	455 args = parser.parse_args()
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	456 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	457 args.input = args.positional_arg
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	458 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	459 parser.error('no input specified')
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	460
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	461 if six.PY2:
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	462 # The argparse.FileType wrapper doesn't support an encoding
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	463 # 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	464 # 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	465 # respective libraries.
107 ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	466 #
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	467 # One option is using codecs, but the codecs' writelines()
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	468 # method doesn't support streaming but collects all output and
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	469 # writes at once (see Python issues #5445 and #21910). On the
b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	470 # other hand the io module is slower (though not
b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	471 # significantly).
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	472
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	473 # args.output = codecs.getwriter('utf-8')(args.output)
107 ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	474 # def fixed_writelines(iter, self=args.output):
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	475 # for i in iter:
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	476 # self.write(i)
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	477 # args.output.writelines = fixed_writelines
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	478
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	479 args.output.close()
109 ea3bc0b9a3d9 fix (again) output encoding Jan Kanis <jan.code@jankanis.nl> parents: 107 diff changeset	480 args.output = io.open(args.output.name, 'w', encoding='utf-8')
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	481
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	482 templatedir, templatename = path.split(args.template.name)
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	483 args.template.close()
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	484 if not templatedir:
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	485 templatedir = '.'
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	486
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	487 defaultentry = genelinks_entry(args.dbname, args.genelink_template)
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	488 if args.db_config_dir is None:
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	489 genelinks = defaultdict(lambda: defaultentry)
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	490 elif not path.isdir(args.db_config_dir):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	491 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	492 else:
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	493 genelinks = read_blastdb(args.db_config_dir, default=defaultentry)
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	494
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	495 b = BlastVisualize(args.input, templatedir, templatename, genelinks=genelinks)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	496 b.render(args.output)
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	497 args.output.close()
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	498
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	499
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	500 if __name__ == '__main__':
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	501 main()
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	502

Mercurial > repos > jankanis > blast2html

annotate blast2html.py @ 120:2729c2326235