annotate blast2html.py @ 85:2edb77030a9e py2.6

re-include backed out revisions and update version numbers
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 24 Jun 2014 11:14:52 +0200
parents 9fb1a7d67317
children 4378d11f0ed7
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1 #!/usr/bin/env python3
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2 # -*- coding: utf-8 -*-
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3
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4 # Actually this program works with both python 2 and 3, tested against python 2.6
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5
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6 # Copyright The Hyve B.V. 2014
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7 # License: GPL version 3 or (at your option) any higher version
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8
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9 from __future__ import unicode_literals, division
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10
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11 import sys
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12 import math
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13 import warnings
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14 import six, codecs
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15 from six.moves import builtins
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16 from os import path
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17 from itertools import repeat
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18 import argparse
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19 from lxml import objectify
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20 import jinja2
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22
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23
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24 _filters = dict(float='float')
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25 def filter(func_or_name):
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26 "Decorator to register a function as filter in the current jinja environment"
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27 if isinstance(func_or_name, six.string_types):
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28 def inner(func):
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29 _filters[func_or_name] = func.__name__
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30 return func
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31 return inner
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32 else:
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33 _filters[func_or_name.__name__] = func_or_name.__name__
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34 return func_or_name
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36
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37 def color_idx(length):
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38 if length < 40:
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39 return 0
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40 elif length < 50:
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41 return 1
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42 elif length < 80:
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43 return 2
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44 elif length < 200:
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45 return 3
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46 return 4
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47
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48 @filter
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49 def fmt(val, fmt):
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50 return format(float(val), fmt)
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51
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52 @filter
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53 def numfmt(val):
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54 """Format numbers in decimal notation, but without excessive trailing 0's.
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55 Default python float formatting will use scientific notation for some values,
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56 or append trailing zeros with the 'f' format type, and the number of digits differs
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57 between python 2 and 3."""
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58 fpart, ipart = math.modf(val)
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59 if fpart == 0:
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60 return str(int(val))
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61 # round to 10 to get identical representations in python 2 and 3
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62 s = format(round(val, 10), '.10f').rstrip('0')
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63 if s[-1] == '.':
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64 s += '0'
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65 return s
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66
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67 @filter
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68 def firsttitle(hit):
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69 return hit.Hit_def.text.split('>')[0]
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71 @filter
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72 def othertitles(hit):
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73 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
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74 id_titles = hit.Hit_def.text.split('>')
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76 titles = []
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77 for t in id_titles[1:]:
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78 fullid, title = t.split(' ', 1)
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79 hitid, id = fullid.split('|', 2)[1:3]
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80 titles.append(dict(id = id,
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81 hitid = hitid,
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82 fullid = fullid,
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83 title = title))
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84 return titles
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85
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86 @filter
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87 def hitid(hit):
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88 hitid = hit.Hit_id.text
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89 s = hitid.split('|', 2)
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90 if len(s) >= 2:
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91 return s[1]
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92 return hitid
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93
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94 @filter
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95 def seqid(hit):
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96 hitid = hit.Hit_id.text
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97 s = hitid.split('|', 2)
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98 if len(s) >= 3:
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99 return s[2]
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100 return hitid
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101
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102
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103 @filter
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104 def alignment_pre(hsp):
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105 """Create the preformatted alignment blocks"""
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106
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107 # line break length
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108 linewidth = 60
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109
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110 qfrom = int(hsp['Hsp_query-from'])
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111 qto = int(hsp['Hsp_query-to'])
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112 qframe = int(hsp['Hsp_query-frame'])
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113 hfrom = int(hsp['Hsp_hit-from'])
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114 hto = int(hsp['Hsp_hit-to'])
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115 hframe = int(hsp['Hsp_hit-frame'])
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116
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117 qseq = hsp.Hsp_qseq.text
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118 midline = hsp.Hsp_midline.text
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119 hseq = hsp.Hsp_hseq.text
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120
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121 if not qframe in (1, -1):
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122 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))
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123 qframe = -1 if qframe < 0 else 1
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124 if not hframe in (1, -1):
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125 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))
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126 hframe = -1 if hframe < 0 else 1
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127
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128 def split(txt):
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129 return [txt[i:i+linewidth] for i in range(0, len(txt), linewidth)]
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130
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131 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), linewidth)):
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132 yield (
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133 "Query {0:>7} {1} {2}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) +
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134 " {0:7} {1}\n".format('', mid) +
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135 "Subject{0:>7} {1} {2}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe)
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136 )
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137
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138 if qfrom+(len(qseq)-1)*qframe != qto:
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139 warnings.warn("Error in BlastXML input: Hsp node {0} qseq length mismatch: from {1} to {2} length {3}".format(
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140 nodeid(hsp), qfrom, qto, len(qseq)))
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diff changeset
141 if hfrom+(len(hseq)-1)*hframe != hto:
73
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diff changeset
142 warnings.warn("Error in BlastXML input: Hsp node {0} hseq length mismatch: from {1} to {2} length {3}".format(
67
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
143 nodeid(hsp), hfrom, hto, len(hseq)))
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diff changeset
144
19c48f2ec775 wrap alignments if they are too long
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diff changeset
145
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diff changeset
146
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diff changeset
147 @filter('len')
19
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diff changeset
148 def blastxml_len(node):
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diff changeset
149 if node.tag == 'Hsp':
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diff changeset
150 return int(node['Hsp_align-len'])
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diff changeset
151 elif node.tag == 'Iteration':
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diff changeset
152 return int(node['Iteration_query-len'])
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diff changeset
153 raise Exception("Unknown XML node type: "+node.tag)
10
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diff changeset
154
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diff changeset
155 @filter
53
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diff changeset
156 def nodeid(node):
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diff changeset
157 id = []
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diff changeset
158 if node.tag == 'Hsp':
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diff changeset
159 id.insert(0, node.Hsp_num.text)
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diff changeset
160 node = node.getparent().getparent()
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diff changeset
161 assert node.tag == 'Hit'
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diff changeset
162 if node.tag == 'Hit':
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diff changeset
163 id.insert(0, node.Hit_num.text)
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diff changeset
164 node = node.getparent().getparent()
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diff changeset
165 assert node.tag == 'Iteration'
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diff changeset
166 if node.tag == 'Iteration':
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diff changeset
167 id.insert(0, node['Iteration_iter-num'].text)
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diff changeset
168 return '-'.join(id)
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diff changeset
169 raise ValueError("The nodeid filter can only be applied to Hsp, Hit or Iteration nodes in a BlastXML document")
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diff changeset
170
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diff changeset
171
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diff changeset
172 @filter
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diff changeset
173 def asframe(frame):
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diff changeset
174 if frame == 1:
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diff changeset
175 return 'Plus'
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176 elif frame == -1:
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diff changeset
177 return 'Minus'
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diff changeset
178 raise Exception("frame should be either +1 or -1")
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diff changeset
179
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180 def genelink(hit, type='genbank', hsp=None):
73
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diff changeset
181 if not isinstance(hit, six.string_types):
12
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diff changeset
182 hit = hitid(hit)
73
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diff changeset
183 link = "http://www.ncbi.nlm.nih.gov/nucleotide/{0}?report={1}&log$=nuclalign".format(hit, type)
12
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diff changeset
184 if hsp != None:
73
67b1a319c6dc First go at 2.6 compatibility
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diff changeset
185 link += "&from={0}&to={1}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
16
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diff changeset
186 return link
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parents: 15
diff changeset
187
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diff changeset
188
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diff changeset
189 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139
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190 # 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
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parents: 5
diff changeset
191
74
03e044b5bcc2 fix escaping of javascript literals
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diff changeset
192 # The r'\u0027' syntax doesn't work the way we need to in python 2.6 with unicode_literals
16
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diff changeset
193 _base_js_escapes = (
74
03e044b5bcc2 fix escaping of javascript literals
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diff changeset
194 ('\\', '\\u005C'),
03e044b5bcc2 fix escaping of javascript literals
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diff changeset
195 ('\'', '\\u0027'),
03e044b5bcc2 fix escaping of javascript literals
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diff changeset
196 ('"', '\\u0022'),
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diff changeset
197 # ('>', '\\u003E'),
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diff changeset
198 # ('<', '\\u003C'),
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diff changeset
199 # ('&', '\\u0026'),
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parents: 73
diff changeset
200 # ('=', '\\u003D'),
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parents: 73
diff changeset
201 # ('-', '\\u002D'),
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parents: 73
diff changeset
202 # (';', '\\u003B'),
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parents: 73
diff changeset
203 (u'\u2028', '\\u2028'),
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parents: 73
diff changeset
204 (u'\u2029', '\\u2029')
16
db7e4ee3be03 fix validation, reindent
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parents: 15
diff changeset
205 )
db7e4ee3be03 fix validation, reindent
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parents: 15
diff changeset
206
db7e4ee3be03 fix validation, reindent
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parents: 15
diff changeset
207 # Escape every ASCII character with a value less than 32. This is
18
4434ffab721a add a parameter for the template
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diff changeset
208 # needed a.o. to prevent html parsers from jumping out of javascript
16
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parents: 15
diff changeset
209 # parsing mode.
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parents: 15
diff changeset
210 _js_escapes = (_base_js_escapes +
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
211 tuple(('%c' % z, '\\u%04X' % z) for z in range(32)))
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parents: 15
diff changeset
212
db7e4ee3be03 fix validation, reindent
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parents: 15
diff changeset
213 @filter
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parents: 15
diff changeset
214 def js_string_escape(value):
72
6ecbfebb9dd9 doc changes
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parents: 71
diff changeset
215 """
6ecbfebb9dd9 doc changes
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parents: 71
diff changeset
216 Javascript string literal escape. Note that this only escapes data
6ecbfebb9dd9 doc changes
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parents: 71
diff changeset
217 for embedding within javascript string literals, not in general
6ecbfebb9dd9 doc changes
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parents: 71
diff changeset
218 javascript snippets.
6ecbfebb9dd9 doc changes
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parents: 71
diff changeset
219 """
16
db7e4ee3be03 fix validation, reindent
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parents: 15
diff changeset
220
73
67b1a319c6dc First go at 2.6 compatibility
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parents: 72
diff changeset
221 value = six.text_type(value)
16
db7e4ee3be03 fix validation, reindent
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parents: 15
diff changeset
222
db7e4ee3be03 fix validation, reindent
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parents: 15
diff changeset
223 for bad, good in _js_escapes:
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parents: 15
diff changeset
224 value = value.replace(bad, good)
db7e4ee3be03 fix validation, reindent
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parents: 15
diff changeset
225
db7e4ee3be03 fix validation, reindent
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parents: 15
diff changeset
226 return value
5
1df2bfce5c24 first features are working, partial match table
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parents:
diff changeset
227
19
67ddcb807b7d make it work with multiple queries
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parents: 18
diff changeset
228 @filter
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parents: 18
diff changeset
229 def hits(result):
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parents: 18
diff changeset
230 # sort hits by longest hotspot first
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parents: 18
diff changeset
231 return sorted(result.Iteration_hits.findall('Hit'),
67ddcb807b7d make it work with multiple queries
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parents: 18
diff changeset
232 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp),
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parents: 18
diff changeset
233 reverse=True)
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parents: 18
diff changeset
234
7
9e7927673089 intermediate commit before converting some tables to divs
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parents: 5
diff changeset
235
5
1df2bfce5c24 first features are working, partial match table
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parents:
diff changeset
236
12
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parents: 11
diff changeset
237 class BlastVisualize:
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parents: 11
diff changeset
238
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diff changeset
239 colors = ('black', 'blue', 'green', 'magenta', 'red')
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diff changeset
240
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diff changeset
241 max_scale_labels = 10
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diff changeset
242
18
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diff changeset
243 def __init__(self, input, templatedir, templatename):
12
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diff changeset
244 self.input = input
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diff changeset
245 self.templatename = templatename
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diff changeset
246
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diff changeset
247 self.blast = objectify.parse(self.input).getroot()
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9fb1a7d67317 remove unneeded encoding parameter
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parents: 78
diff changeset
248 self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
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diff changeset
249 self.environment = jinja2.Environment(loader=self.loader,
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diff changeset
250 lstrip_blocks=True, trim_blocks=True, autoescape=True)
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diff changeset
251
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diff changeset
252 self._addfilters(self.environment)
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parents: 18
diff changeset
253
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diff changeset
254
19
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diff changeset
255 def _addfilters(self, environment):
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parents: 18
diff changeset
256 for filtername, funcname in _filters.items():
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parents: 18
diff changeset
257 try:
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diff changeset
258 environment.filters[filtername] = getattr(self, funcname)
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parents: 18
diff changeset
259 except AttributeError:
75
4d2c25baf5a3 Fix rounding errors
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parents: 74
diff changeset
260 try:
4d2c25baf5a3 Fix rounding errors
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parents: 74
diff changeset
261 environment.filters[filtername] = globals()[funcname]
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diff changeset
262 except KeyError:
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diff changeset
263 environment.filters[filtername] = getattr(builtins, funcname)
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diff changeset
264
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diff changeset
265 def render(self, output):
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diff changeset
266 template = self.environment.get_template(self.templatename)
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diff changeset
267
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diff changeset
268 params = (('Query ID', self.blast["BlastOutput_query-ID"]),
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diff changeset
269 ('Query definition', self.blast["BlastOutput_query-def"]),
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diff changeset
270 ('Query length', self.blast["BlastOutput_query-len"]),
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diff changeset
271 ('Program', self.blast.BlastOutput_version),
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diff changeset
272 ('Database', self.blast.BlastOutput_db),
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diff changeset
273 )
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diff changeset
274
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diff changeset
275 result = template.render(blast=self.blast,
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diff changeset
276 iterations=self.blast.BlastOutput_iterations.Iteration,
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diff changeset
277 colors=self.colors,
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diff changeset
278 genelink=genelink,
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diff changeset
279 params=params)
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diff changeset
280 if six.PY2:
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diff changeset
281 result = result.encode('utf-8')
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diff changeset
282 output.write(result)
12
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283
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284 @filter
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285 def match_colors(self, result):
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286 """
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287 An iterator that yields lists of length-color pairs.
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288 """
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289
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290 query_length = blastxml_len(result)
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291
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292 percent_multiplier = 100 / query_length
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293
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294 for hit in hits(result):
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295 # sort hotspots from short to long, so we can overwrite index colors of
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296 # short matches with those of long ones.
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297 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp))
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298 table = bytearray([255]) * query_length
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299 for hsp in hotspots:
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300 frm = hsp['Hsp_query-from'] - 1
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301 to = int(hsp['Hsp_query-to'])
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302 table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm)
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303
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304 matches = []
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305 last = table[0]
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306 count = 0
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307 for i in range(query_length):
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308 if table[i] == last:
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309 count += 1
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310 continue
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311 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
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312 last = table[i]
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313 count = 1
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314 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
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315
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316 yield dict(colors=matches, hit=hit, defline=firsttitle(hit))
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317
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318 @filter
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319 def queryscale(self, result):
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320 query_length = blastxml_len(result)
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321 skip = math.ceil(query_length / self.max_scale_labels)
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322 percent_multiplier = 100 / query_length
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323 for i in range(1, query_length+1):
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324 if i % skip == 0:
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325 yield dict(label = i, width = skip * percent_multiplier)
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326 if query_length % skip != 0:
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327 yield dict(label = query_length,
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328 width = (query_length % skip) * percent_multiplier)
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329
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330 @filter
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331 def hit_info(self, result):
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332
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333 query_length = blastxml_len(result)
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334
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335 for hit in hits(result):
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336 hsps = hit.Hit_hsps.Hsp
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337
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338 cover = [False] * query_length
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339 for hsp in hsps:
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340 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp))
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341 cover_count = cover.count(True)
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342
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343 def hsp_val(path):
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344 return (float(hsp[path]) for hsp in hsps)
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345
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346 yield dict(hit = hit,
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347 title = firsttitle(hit),
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348 maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))),
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349 totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
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350 cover = "{0:.0%}".format(cover_count / query_length),
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351 e_value = "{0:.4g}".format(min(hsp_val('Hsp_evalue'))),
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352 # FIXME: is this the correct formula vv?
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353 # float(...) because non-flooring division doesn't work with lxml elements in python 2.6
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354 ident = "{0:.0%}".format(float(min(float(hsp.Hsp_identity) / blastxml_len(hsp) for hsp in hsps))),
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355 accession = hit.Hit_accession)
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356
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357
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358 def main():
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359 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')
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360
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361 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
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362 usage="{0} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
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363 input_group = parser.add_mutually_exclusive_group(required=True)
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364 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
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365 help='The input Blast XML file, same as -i/--input')
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366 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'),
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367 help='The input Blast XML file')
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368 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
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369 help='The output html file')
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370 # We just want the file name here, so jinja can open the file
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371 # itself. But it is easier to just use a FileType so argparse can
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diff changeset
372 # handle the errors. This introduces a small race condition when
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373 # jinja later tries to re-open the template file, but we don't
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374 # care too much.
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375 parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template,
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376 help='The template file to use. Defaults to blast_html.html.jinja')
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377
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378 args = parser.parse_args()
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379 if args.input == None:
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380 args.input = args.positional_arg
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381 if args.input == None:
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382 parser.error('no input specified')
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383
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diff changeset
384 templatedir, templatename = path.split(args.template.name)
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diff changeset
385 args.template.close()
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diff changeset
386 if not templatedir:
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387 templatedir = '.'
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diff changeset
388
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diff changeset
389 b = BlastVisualize(args.input, templatedir, templatename)
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diff changeset
390 b.render(args.output)
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diff changeset
391
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diff changeset
392
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diff changeset
393 if __name__ == '__main__':
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diff changeset
394 main()
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diff changeset
395