blast2html: blast2html.py annotate

annotate blast2html.py @ 101:e780606b7c25 draft

test new command line parameters, fix small bug

author	Jan Kanis <jan.code@jankanis.nl>
date	Mon, 30 Jun 2014 17:51:56 +0200
parents	02b795b784e1
children	8f02008a5f20

rev	line source
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	1 #!/usr/bin/env python3
52 bfc82a8aa3c9 unicodify python sources Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	2 # -- coding: utf-8 --
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	3
77 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	4 # Actually this program works with both python 2 and 3, tested against python 2.6
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	5
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	6 # Copyright The Hyve B.V. 2014
74 6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	7 # License: GPL version 3 or (at your option) any higher version
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	8
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	9 from __future__ import unicode_literals, division
52 bfc82a8aa3c9 unicodify python sources Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	10
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	11 import sys
9 9e7927673089 intermediate commit before converting some tables to divs Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	12 import math
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	13 import warnings
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	14 import six, codecs
77 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	15 from six.moves import builtins
20 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	16 from os import path
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	17 from itertools import repeat
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	18 from collections import defaultdict
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	19 import argparse
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	20 from lxml import objectify
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	21 import jinja2
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	22
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	23 builtin_str = str
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	24 str = six.text_type
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	25
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	26
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	27
78 7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	28 _filters = dict(float='float')
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	29 def filter(func_or_name):
13 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 12 diff changeset	30 "Decorator to register a function as filter in the current jinja environment"
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	31 if isinstance(func_or_name, six.string_types):
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	32 def inner(func):
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	33 _filters[func_or_name] = func.__name__
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	34 return func
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	35 return inner
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	36 else:
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	37 _filters[func_or_name.__name__] = func_or_name.__name__
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	38 return func_or_name
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	39
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	40
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	41 def color_idx(length):
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	42 if length < 40:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	43 return 0
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	44 elif length < 50:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	45 return 1
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	46 elif length < 80:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	47 return 2
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	48 elif length < 200:
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	49 return 3
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	50 return 4
1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	51
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	52 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	53 def fmt(val, fmt):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	54 return format(float(val), fmt)
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	55
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	56 @filter
78 7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	57 def numfmt(val):
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	58 """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: 77 diff changeset	59 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: 77 diff changeset	60 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: 77 diff changeset	61 between python 2 and 3."""
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	62 fpart, ipart = math.modf(val)
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	63 if fpart == 0:
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	64 return str(int(val))
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	65 # 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: 77 diff changeset	66 s = format(round(val, 10), '.10f').rstrip('0')
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	67 if s[-1] == '.':
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	68 s += '0'
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	69 return s
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	70
7d0d46168fd5 Format all numbers in a predictable way Jan Kanis <jan.code@jankanis.nl> parents: 77 diff changeset	71 @filter
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	72 def firsttitle(hit):
99 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	73 return str(hit.Hit_def).split('>')[0]
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	74
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	75 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	76 def othertitles(hit):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	77 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
99 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	78 id_titles = str(hit.Hit_def).split('>')
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	79
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	80 titles = []
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	81 for t in id_titles[1:]:
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	82 id, title = t.split(' ', 1)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	83 titles.append(argparse.Namespace(Hit_id = id,
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	84 Hit_def = title,
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	85 Hit_accession = '',
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	86 getroottree = hit.getroottree))
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	87 return titles
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	88
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	89 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	90 def hitid(hit):
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	91 return str(hit.Hit_id)
26 c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values Jan Kanis <jan.code@jankanis.nl> parents: 25 diff changeset	92
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	93
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	94 @filter
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	95 def alignment_pre(hsp):
70 fa8a93bdefd7 fix bug in calculations of alignment end Jan Kanis <jan.code@jankanis.nl> parents: 69 diff changeset	96 """Create the preformatted alignment blocks"""
73 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	97
371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	98 # line break length
371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	99 linewidth = 60
69 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	100
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	101 qfrom = int(hsp['Hsp_query-from'])
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	102 qto = int(hsp['Hsp_query-to'])
71 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 70 diff changeset	103 qframe = int(hsp['Hsp_query-frame'])
69 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	104 hfrom = int(hsp['Hsp_hit-from'])
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	105 hto = int(hsp['Hsp_hit-to'])
71 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 70 diff changeset	106 hframe = int(hsp['Hsp_hit-frame'])
73 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	107
69 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	108 qseq = hsp.Hsp_qseq.text
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	109 midline = hsp.Hsp_midline.text
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	110 hseq = hsp.Hsp_hseq.text
71 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 70 diff changeset	111
73 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	112 if not qframe in (1, -1):
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	113 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))
71 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 70 diff changeset	114 qframe = -1 if qframe < 0 else 1
73 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	115 if not hframe in (1, -1):
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	116 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))
71 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 70 diff changeset	117 hframe = -1 if hframe < 0 else 1
69 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	118
71 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 70 diff changeset	119 def split(txt):
73 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	120 return [txt[i:i+linewidth] for i in range(0, len(txt), linewidth)]
71 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 70 diff changeset	121
73 371cd585e459 refactor Jan Kanis <jan.code@jankanis.nl> parents: 71 diff changeset	122 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), linewidth)):
69 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	123 yield (
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	124 "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: 74 diff changeset	125 " {0:7} {1}\n".format('', mid) +
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	126 "Subject{0:>7} {1} {2}".format(hfrom+offsethframe, hs, hfrom+(offset+len(hs)-1)hframe)
69 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	127 )
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	128
71 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 70 diff changeset	129 if qfrom+(len(qseq)-1)*qframe != qto:
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	130 warnings.warn("Error in BlastXML input: Hsp node {0} qseq length mismatch: from {1} to {2} length {3}".format(
69 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	131 nodeid(hsp), qfrom, qto, len(qseq)))
71 0c4ac210068b handle reverse matches Jan Kanis <jan.code@jankanis.nl> parents: 70 diff changeset	132 if hfrom+(len(hseq)-1)*hframe != hto:
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	133 warnings.warn("Error in BlastXML input: Hsp node {0} hseq length mismatch: from {1} to {2} length {3}".format(
69 19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	134 nodeid(hsp), hfrom, hto, len(hseq)))
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	135
19c48f2ec775 wrap alignments if they are too long Jan Kanis <jan.code@jankanis.nl> parents: 55 diff changeset	136
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	137
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	138 @filter('len')
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	139 def blastxml_len(node):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	140 if node.tag == 'Hsp':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	141 return int(node['Hsp_align-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	142 elif node.tag == 'Iteration':
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	143 return int(node['Iteration_query-len'])
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	144 raise Exception("Unknown XML node type: "+node.tag)
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	145
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	146 @filter
55 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	147 def nodeid(node):
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	148 id = []
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	149 if node.tag == 'Hsp':
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	150 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: 53 diff changeset	151 node = node.getparent().getparent()
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	152 assert node.tag == 'Hit'
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	153 if node.tag == 'Hit':
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	154 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: 53 diff changeset	155 node = node.getparent().getparent()
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	156 assert node.tag == 'Iteration'
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	157 if node.tag == 'Iteration':
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	158 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: 53 diff changeset	159 return '-'.join(id)
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	160 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: 53 diff changeset	161
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	162
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	163 @filter
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	164 def asframe(frame):
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	165 if frame == 1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	166 return 'Plus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	167 elif frame == -1:
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	168 return 'Minus'
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	169 raise Exception("frame should be either +1 or -1")
2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	170
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	171 # def genelink(hit, type='genbank', hsp=None):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	172 # if not isinstance(hit, six.string_types):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	173 # hit = hitid(hit)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	174 # 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: 81 diff changeset	175 # if hsp != None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	176 # 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: 81 diff changeset	177 # return link
18 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	178
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	179
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	180 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	181 # I've removed the html escapes, since html escaping is already being performed by the template engine.
9 9e7927673089 intermediate commit before converting some tables to divs Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	182
76 03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	183 # The r'\u0027' syntax doesn't work the way we need to in python 2.6 with unicode_literals
18 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	184 _base_js_escapes = (
76 03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	185 ('\\', '\\u005C'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	186 ('\'', '\\u0027'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	187 ('"', '\\u0022'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	188 # ('>', '\\u003E'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	189 # ('<', '\\u003C'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	190 # ('&', '\\u0026'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	191 # ('=', '\\u003D'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	192 # ('-', '\\u002D'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	193 # (';', '\\u003B'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	194 (u'\u2028', '\\u2028'),
03e044b5bcc2 fix escaping of javascript literals Jan Kanis <jan.code@jankanis.nl> parents: 75 diff changeset	195 (u'\u2029', '\\u2029')
18 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	196 )
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	197
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	198 # Escape every ASCII character with a value less than 32. This is
20 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	199 # needed a.o. to prevent html parsers from jumping out of javascript
18 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	200 # parsing mode.
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	201 _js_escapes = (_base_js_escapes +
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	202 tuple(('%c' % z, '\\u%04X' % z) for z in range(32)))
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	203
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	204 @filter
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	205 def js_string_escape(value):
74 6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	206 """
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	207 Javascript string literal escape. Note that this only escapes data
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	208 for embedding within javascript string literals, not in general
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	209 javascript snippets.
6ecbfebb9dd9 doc changes Jan Kanis <jan.code@jankanis.nl> parents: 73 diff changeset	210 """
18 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	211
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	212 value = str(value)
18 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	213
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	214 for bad, good in _js_escapes:
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	215 value = value.replace(bad, good)
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	216
db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	217 return value
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	218
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	219 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	220 def hits(result):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	221 # sort hits by longest hotspot first
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	222 return sorted(result.Iteration_hits.findall('Hit'),
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	223 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp),
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	224 reverse=True)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	225
9 9e7927673089 intermediate commit before converting some tables to divs Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	226
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	227
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	228 class BlastVisualize:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	229
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	230 colors = ('black', 'blue', 'green', 'magenta', 'red')
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	231
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	232 max_scale_labels = 10
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	233
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	234 def __init__(self, input, templatedir, templatename, genelinks={}):
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	235 self.input = input
20 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	236 self.templatename = templatename
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	237 self.genelinks = genelinks
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	238
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	239 self.blast = objectify.parse(self.input).getroot()
81 9fb1a7d67317 remove unneeded encoding parameter Jan Kanis <jan.code@jankanis.nl> parents: 80 diff changeset	240 self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	241 self.environment = jinja2.Environment(loader=self.loader,
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	242 lstrip_blocks=True, trim_blocks=True, autoescape=True)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	243
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	244 self._addfilters(self.environment)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	245
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	246
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	247 def _addfilters(self, environment):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	248 for filtername, funcname in _filters.items():
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	249 try:
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	250 environment.filters[filtername] = getattr(self, funcname)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	251 except AttributeError:
77 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	252 try:
4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	253 environment.filters[filtername] = globals()[funcname]
4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	254 except KeyError:
4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	255 environment.filters[filtername] = getattr(builtins, funcname)
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	256
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	257 def render(self, output):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	258 template = self.environment.get_template(self.templatename)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	259
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	260 params = (('Query ID', self.blast["BlastOutput_query-ID"]),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	261 ('Query definition', self.blast["BlastOutput_query-def"]),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	262 ('Query length', self.blast["BlastOutput_query-len"]),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	263 ('Program', self.blast.BlastOutput_version),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	264 ('Database', self.blast.BlastOutput_db),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	265 )
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	266
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	267 result = template.render(blast=self.blast,
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	268 iterations=self.blast.BlastOutput_iterations.Iteration,
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	269 colors=self.colors,
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	270 params=params)
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	271 if six.PY2:
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	272 result = result.encode('utf-8')
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	273 output.write(result)
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	274
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	275 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	276 def match_colors(self, result):
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	277 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	278 An iterator that yields lists of length-color pairs.
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	279 """
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	280
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	281 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	282
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	283 percent_multiplier = 100 / query_length
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	284
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	285 for hit in hits(result):
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	286 # sort hotspots from short to long, so we can overwrite index colors of
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	287 # short matches with those of long ones.
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	288 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp))
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	289 table = bytearray([255]) * query_length
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	290 for hsp in hotspots:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	291 frm = hsp['Hsp_query-from'] - 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	292 to = int(hsp['Hsp_query-to'])
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	293 table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm)
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	294
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	295 matches = []
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	296 last = table[0]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	297 count = 0
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	298 for i in range(query_length):
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	299 if table[i] == last:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	300 count += 1
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	301 continue
18 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	302 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	303 last = table[i]
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	304 count = 1
18 db7e4ee3be03 fix validation, reindent Jan Kanis <jan.code@jankanis.nl> parents: 17 diff changeset	305 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	306
55 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	307 yield dict(colors=matches, hit=hit, defline=firsttitle(hit))
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	308
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	309 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	310 def queryscale(self, result):
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	311 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	312 skip = math.ceil(query_length / self.max_scale_labels)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	313 percent_multiplier = 100 / query_length
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	314 for i in range(1, query_length+1):
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	315 if i % skip == 0:
25 6995a6f34f3f fix sectioning, add footer Jan Kanis <jan.code@jankanis.nl> parents: 24 diff changeset	316 yield dict(label = i, width = skip * percent_multiplier)
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	317 if query_length % skip != 0:
22 53cd304c5f26 Add index for multiple results; fix layout of query ruler for edge case Jan Kanis <jan.code@jankanis.nl> parents: 21 diff changeset	318 yield dict(label = query_length,
25 6995a6f34f3f fix sectioning, add footer Jan Kanis <jan.code@jankanis.nl> parents: 24 diff changeset	319 width = (query_length % skip) * percent_multiplier)
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	320
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	321 @filter
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	322 def hit_info(self, result):
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	323
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	324 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	325
67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	326 for hit in hits(result):
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	327 hsps = hit.Hit_hsps.Hsp
9 9e7927673089 intermediate commit before converting some tables to divs Jan Kanis <jan.code@jankanis.nl> parents: 7 diff changeset	328
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	329 cover = [False] * query_length
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	330 for hsp in hsps:
21 67ddcb807b7d make it work with multiple queries Jan Kanis <jan.code@jankanis.nl> parents: 20 diff changeset	331 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp))
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	332 cover_count = cover.count(True)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	333
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	334 def hsp_val(path):
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	335 return (float(hsp[path]) for hsp in hsps)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	336
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	337 yield dict(hit = hit,
77 4d2c25baf5a3 Fix rounding errors Jan Kanis <jan.code@jankanis.nl> parents: 76 diff changeset	338 title = firsttitle(hit),
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	339 maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))),
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	340 totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	341 cover = "{0:.0%}".format(cover_count / query_length),
67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	342 e_value = "{0:.4g}".format(min(hsp_val('Hsp_evalue'))),
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	343 # FIXME: is this the correct formula vv?
80 c0804e6443c6 comment Jan Kanis <jan.code@jankanis.nl> parents: 78 diff changeset	344 # float(...) because non-flooring division doesn't work with lxml elements in python 2.6
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	345 ident = "{0:.0%}".format(float(min(float(hsp.Hsp_identity) / blastxml_len(hsp) for hsp in hsps))))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	346
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	347 @filter
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	348 def genelink(self, hit, text=None, clas=None, display_nolink=True):
99 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	349 """Create a html link from a hit node to a configured gene bank webpage.
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	350 text: The text of the link, defaults to the hit_id
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	351 clas: extra css classes that will be added to the <a> element
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	352 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: 98 diff changeset	353 """
02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	354
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	355 if text is None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	356 text = hitid(hit)
99 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	357
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	358 db = hit.getroottree().getroot().BlastOutput_db
99 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	359
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	360 if isinstance(self.genelinks, six.string_types):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	361 template = self.genelinks
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	362 else:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	363 template = self.genelinks.get(db)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	364 if template is None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	365 return text if display_nolink else ''
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	366 args = dict(id=hitid(hit).split('\|'),
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	367 fullid=hitid(hit),
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	368 defline=str(hit.Hit_def).split('\|'),
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	369 fulldefline=str(hit.Hit_def),
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	370 accession=str(hit.Hit_accession))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	371 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	372 link = template.format(**args)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	373 except Exception as e:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	374 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: 81 diff changeset	375 return text if display_nolink else ''
99 02b795b784e1 fix bug; add comments Jan Kanis <jan.code@jankanis.nl> parents: 98 diff changeset	376
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	377 classattr = 'class="{}" '.format(jinja2.escape(clas)) if clas is not None else ''
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	378 return jinja2.Markup("<a {}href=\"{}\">{}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text)))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	379
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	380
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	381 def read_genelinks(dir):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	382 links = {}
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	383 for f in ('blastdb.loc', 'blastdb_p.loc', 'blastdb_d.loc'):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	384 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	385 f = open(path.join(dir, f))
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	386 for l in f.readlines():
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	387 if l.strip().startswith('#'):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	388 continue
101 e780606b7c25 test new command line parameters, fix small bug Jan Kanis <jan.code@jankanis.nl> parents: 99 diff changeset	389 line = l.rstrip('\n').split('\t')
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	390 try:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	391 links[line[2]] = line[3]
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	392 except IndexError:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	393 continue
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	394 f.close()
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	395 except OSError:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	396 continue
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	397 if not links:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	398 warnings.warn("No gene bank link templates found")
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	399 return links
12 2fbdf2eb27b4 All data is displayed now, still some formatting to do Jan Kanis <jan.code@jankanis.nl> parents: 9 diff changeset	400
29 4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy Jan Kanis <jan.code@jankanis.nl> parents: 26 diff changeset	401
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	402 def main():
29 4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy Jan Kanis <jan.code@jankanis.nl> parents: 26 diff changeset	403 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	404
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	405 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
75 67b1a319c6dc First go at 2.6 compatibility Jan Kanis <jan.code@jankanis.nl> parents: 74 diff changeset	406 usage="{0} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	407 input_group = parser.add_mutually_exclusive_group(required=True)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	408 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	409 help='The input Blast XML file, same as -i/--input')
55 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	410 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'),
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	411 help='The input Blast XML file')
55 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	412 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	413 help='The output html file')
20 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	414 # We just want the file name here, so jinja can open the file
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	415 # itself. But it is easier to just use a FileType so argparse can
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	416 # handle the errors. This introduces a small race condition when
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	417 # jinja later tries to re-open the template file, but we don't
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	418 # care too much.
55 4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations Jan Kanis <jan.code@jankanis.nl> parents: 53 diff changeset	419 parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template,
20 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	420 help='The template file to use. Defaults to blast_html.html.jinja')
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	421
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	422 dblink_group = parser.add_mutually_exclusive_group()
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	423 dblink_group.add_argument('--genelink-template', default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	424 help="""A link template to link hits to a gene bank webpage. The template string is a
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	425 Python format string. It can contain the following replacement elements: {id[N]}, {fullid},
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	426 {defline[N]}, {fulldefline}, {accession}, where N is a number. id[N] and defline[N] will be
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	427 replaced by the Nth element of the id or defline, where '\|' is the field separator.
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	428
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	429 The default is 'http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	430 which is a link to the NCBI nucleotide database.""")
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	431
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	432 dblink_group.add_argument('--db-config-dir',
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	433 help="""The directory where databases are configured in blastdb*.loc files. These files
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	434 are consulted for creating a gene bank link. The files should be tab-separated tables (with lines
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	435 starting with '#' ignored), where the third field of a line should be a database path and the fourth
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	436 a genebank link template conforming to the --genelink-template option syntax.
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	437
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	438 This option is incompatible with --genelink-template.""")
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	439
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	440 args = parser.parse_args()
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	441 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	442 args.input = args.positional_arg
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	443 if args.input == None:
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	444 parser.error('no input specified')
7 1df2bfce5c24 first features are working, partial match table Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	445
20 4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	446 templatedir, templatename = path.split(args.template.name)
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	447 args.template.close()
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	448 if not templatedir:
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	449 templatedir = '.'
4434ffab721a add a parameter for the template Jan Kanis <jan.code@jankanis.nl> parents: 18 diff changeset	450
98 4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	451 if args.db_config_dir is None:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	452 genelinks = args.genelink_template
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	453 elif not path.isdir(args.db_config_dir):
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	454 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: 81 diff changeset	455 else:
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	456 genelinks = read_genelinks(args.db_config_dir)
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	457
4378d11f0ed7 implement configurable gene bank links Jan Kanis <jan.code@jankanis.nl> parents: 81 diff changeset	458 b = BlastVisualize(args.input, templatedir, templatename, genelinks)
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	459 b.render(args.output)
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	460
13 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 12 diff changeset	461
14 a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	462 if __name__ == '__main__':
a459c754cdb5 add links, refactor, proper commandline arguments Jan Kanis <jan.code@jankanis.nl> parents: 13 diff changeset	463 main()
13 7660519f2dc9 proper layout for alignments, added some links Jan Kanis <jan.code@jankanis.nl> parents: 12 diff changeset	464

Mercurial > repos > jankanis > blast2html

annotate blast2html.py @ 101:e780606b7c25 draft