blast2html: blast2html.py annotate

annotate blast2html.py @ 122:5f104d05aa23

fix python 2.6 issue with array type codes

author	Jan Kanis <jan.code@jankanis.nl>
date	Thu, 31 Jul 2014 17:24:10 +0200
parents	2729c2326235
children	720efb818f1b

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
122 5f104d05aa23 fix python 2.6 issue with array type codes Jan Kanis <jan.code@jankanis.nl> parents: 120 diff changeset	331 # In python 2.6 array doesn't accept unicode type codes, but in 3.4 it requires them
5f104d05aa23 fix python 2.6 issue with array type codes Jan Kanis <jan.code@jankanis.nl> parents: 120 diff changeset	332 cover = array(str('B'), [0]) * 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:
122 5f104d05aa23 fix python 2.6 issue with array type codes Jan Kanis <jan.code@jankanis.nl> parents: 120 diff changeset	334 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = array(str('B'), [1]) * blastxml_len(hsp)
120 2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	335 cover_count = cover.count(1)
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	336
120 2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	337 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	338
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	339 yield dict(hit = hit,
75 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	340 title = firsttitle(hit),
120 2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	341 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	342 e_value = format(float(best_hsp.Hsp_evalue), '.4'),
78 c0804e6443c6 comment Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	343 # 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	344 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	345 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	346 cover = format(cover_count / query_length, '.0%'),
2729c2326235 Fix for Rikilt issue 13 Jan Kanis <jan.code@jankanis.nl> parents: 119 diff changeset	347 )
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	348
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	349 @filter
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	350 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	351 """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	352 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	353 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	354 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	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 db = hit.getroottree().getroot().BlastOutput_db
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	359
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	360 template = self.genelinks[db].template
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	361
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	362 if text is None:
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	363 if text_from == 'hitid':
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	364 text = hitid(hit)
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	365 elif text_from == 'dbname':
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	366 text = self.genelinks[db].dbname
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	367 else:
0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	368 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	369
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	370 if template is None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	371 return text if display_nolink else ''
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	372
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	373 args = dict(id=hitid(hit).split('\|'),
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	374 fullid=hitid(hit),
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	375 defline=str(hit.Hit_def).split(' ', 1)[0].split('\|'),
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	376 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	377 accession=str(hit.Hit_accession))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	378 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	379 link = template.format(**args)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	380 except Exception as e:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	381 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	382 return text if display_nolink else ''
96 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 95 diff changeset	383
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	384 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	385 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	386
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	387
115 0c2a03f9740b make external gene bank name configurable Jan Kanis <jan.code@jankanis.nl> parents: 110 diff changeset	388 genelinks_entry = namedtuple('genelinks_entry', 'dbname template')
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	389 def read_blastdb(dir, default):
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	390 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	391 # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc.
101 5bfaa3ee1f27 better warning message Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	392 files = sorted(glob.glob(path.join(dir, 'blastdb*.loc')))
5bfaa3ee1f27 better warning message Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	393 # reversed, so blastdb.loc will take precedence
5bfaa3ee1f27 better warning message Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	394 for f in reversed(files):
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	395 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	396 f = open(path.join(dir, f))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	397 for l in f.readlines():
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	398 if l.strip().startswith('#'):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	399 continue
98 e780606b7c25 test new command line parameters, fix small bug Jan Kanis <jan.code@jankanis.nl> parents: 96 diff changeset	400 line = l.rstrip('\n').split('\t')
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	401 try:
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	402 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	403 except IndexError:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	404 continue
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	405 f.close()
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	406 except OSError:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	407 continue
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	408 if not links:
103 86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	409 if not files:
86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	410 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	411 else:
86bcf17f50ef improve warning messages Jan Kanis <jan.code@jankanis.nl> parents: 102 diff changeset	412 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	413 return links
10 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	414
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	415
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	416 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	417 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	418
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	419 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	420 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	421 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	422 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	423 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	424 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	425 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	426 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	427 help='The output html file')
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	428 # 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	429 # 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	430 # 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	431 # 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	432 # 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	433 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	434 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	435
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	436 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	437 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	438 parser.add_argument('--genelink-template', metavar='URL_TEMPLATE',
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	439 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	440 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	441 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	442 {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	443 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	444
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	445 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	446 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	447
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	448 parser.add_argument('--db-config-dir',
f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	449 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	450 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	451 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	452 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	453 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	454 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	455
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	456 args = parser.parse_args()
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	457 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	458 args.input = args.positional_arg
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	459 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	460 parser.error('no input specified')
5 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	461
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	462 if six.PY2:
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	463 # The argparse.FileType wrapper doesn't support an encoding
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	464 # 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	465 # 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	466 # respective libraries.
107 ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	467 #
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	468 # One option is using codecs, but the codecs' writelines()
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	469 # method doesn't support streaming but collects all output and
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	470 # writes at once (see Python issues #5445 and #21910). On the
b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	471 # other hand the io module is slower (though not
b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 104 diff changeset	472 # significantly).
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	473
a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	474 # args.output = codecs.getwriter('utf-8')(args.output)
107 ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	475 # def fixed_writelines(iter, self=args.output):
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	476 # for i in iter:
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	477 # self.write(i)
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	478 # args.output.writelines = fixed_writelines
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	479
ee2b105d772a minor fix Jan Kanis <jan.code@jankanis.nl> parents: 105 diff changeset	480 args.output.close()
109 ea3bc0b9a3d9 fix (again) output encoding Jan Kanis <jan.code@jankanis.nl> parents: 107 diff changeset	481 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	482
18 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	483 templatedir, templatename = path.split(args.template.name)
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	484 args.template.close()
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	485 if not templatedir:
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	486 templatedir = '.'
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 16 diff changeset	487
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	488 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	489 if args.db_config_dir is None:
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	490 genelinks = defaultdict(lambda: defaultentry)
95 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	491 elif not path.isdir(args.db_config_dir):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 79 diff changeset	492 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	493 else:
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	494 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	495
116 f5066973029a refactor Jan Kanis <jan.code@jankanis.nl> parents: 115 diff changeset	496 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	497 b.render(args.output)
104 a22c909c9b57 stream output Jan Kanis <jan.code@jankanis.nl> parents: 103 diff changeset	498 args.output.close()
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	499
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	500
12 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	501 if __name__ == '__main__':
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 11 diff changeset	502 main()
11 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 10 diff changeset	503

Mercurial > repos > jankanis > blast2html

annotate blast2html.py @ 122:5f104d05aa23