annotate blast2html.py @ 103:86bcf17f50ef

improve warning messages
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 01 Jul 2014 17:18:09 +0200
parents 87c5402e0ba8
children a22c909c9b57
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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 from collections import defaultdict
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19 import glob
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20 import argparse
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21 from lxml import objectify
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22 import jinja2
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23
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24 builtin_str = str
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25 str = six.text_type
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29 _filters = dict(float='float')
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30 def filter(func_or_name):
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31 "Decorator to register a function as filter in the current jinja environment"
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32 if isinstance(func_or_name, six.string_types):
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33 def inner(func):
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34 _filters[func_or_name] = func.__name__
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35 return func
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36 return inner
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37 else:
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38 _filters[func_or_name.__name__] = func_or_name.__name__
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39 return func_or_name
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41
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42 def color_idx(length):
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43 if length < 40:
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44 return 0
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45 elif length < 50:
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46 return 1
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47 elif length < 80:
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48 return 2
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49 elif length < 200:
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50 return 3
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51 return 4
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52
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53 @filter
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54 def fmt(val, fmt):
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55 return format(float(val), fmt)
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56
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57 @filter
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58 def numfmt(val):
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59 """Format numbers in decimal notation, but without excessive trailing 0's.
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60 Default python float formatting will use scientific notation for some values,
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61 or append trailing zeros with the 'f' format type, and the number of digits differs
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62 between python 2 and 3."""
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63 fpart, ipart = math.modf(val)
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64 if fpart == 0:
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65 return str(int(val))
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66 # round to 10 to get identical representations in python 2 and 3
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67 s = format(round(val, 10), '.10f').rstrip('0')
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68 if s[-1] == '.':
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69 s += '0'
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70 return s
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72 @filter
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73 def firsttitle(hit):
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74 return str(hit.Hit_def).split('>')[0]
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76 @filter
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77 def othertitles(hit):
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78 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
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79 id_titles = str(hit.Hit_def).split('>')
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81 titles = []
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82 for t in id_titles[1:]:
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83 id, title = t.split(' ', 1)
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84 titles.append(argparse.Namespace(Hit_id = id,
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85 Hit_def = title,
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86 Hit_accession = '',
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87 getroottree = hit.getroottree))
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88 return titles
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90 @filter
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91 def hitid(hit):
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92 return str(hit.Hit_id)
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93
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95 @filter
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96 def alignment_pre(hsp):
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97 """Create the preformatted alignment blocks"""
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98
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99 # line break length
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100 linewidth = 60
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101
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102 qfrom = int(hsp['Hsp_query-from'])
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103 qto = int(hsp['Hsp_query-to'])
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104 qframe = int(hsp['Hsp_query-frame'])
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105 hfrom = int(hsp['Hsp_hit-from'])
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106 hto = int(hsp['Hsp_hit-to'])
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107 hframe = int(hsp['Hsp_hit-frame'])
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108
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109 qseq = hsp.Hsp_qseq.text
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110 midline = hsp.Hsp_midline.text
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111 hseq = hsp.Hsp_hseq.text
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112
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113 if not qframe in (1, -1):
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114 warnings.warn("Error in BlastXML input: Hsp node {0} has a Hsp_query-frame of {1}. (should be 1 or -1)".format(nodeid(hsp), qframe))
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115 qframe = -1 if qframe < 0 else 1
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116 if not hframe in (1, -1):
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117 warnings.warn("Error in BlastXML input: Hsp node {0} has a Hsp_hit-frame of {1}. (should be 1 or -1)".format(nodeid(hsp), hframe))
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118 hframe = -1 if hframe < 0 else 1
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119
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120 def split(txt):
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121 return [txt[i:i+linewidth] for i in range(0, len(txt), linewidth)]
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122
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123 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), linewidth)):
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124 yield (
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125 "Query {0:>7} {1} {2}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) +
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126 " {0:7} {1}\n".format('', mid) +
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127 "Subject{0:>7} {1} {2}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe)
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128 )
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129
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130 if qfrom+(len(qseq)-1)*qframe != qto:
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131 warnings.warn("Error in BlastXML input: Hsp node {0} qseq length mismatch: from {1} to {2} length {3}".format(
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132 nodeid(hsp), qfrom, qto, len(qseq)))
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133 if hfrom+(len(hseq)-1)*hframe != hto:
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134 warnings.warn("Error in BlastXML input: Hsp node {0} hseq length mismatch: from {1} to {2} length {3}".format(
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135 nodeid(hsp), hfrom, hto, len(hseq)))
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136
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137
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138
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139 @filter('len')
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140 def blastxml_len(node):
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141 if node.tag == 'Hsp':
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142 return int(node['Hsp_align-len'])
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143 elif node.tag == 'Iteration':
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144 return int(node['Iteration_query-len'])
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145 raise Exception("Unknown XML node type: "+node.tag)
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146
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147 @filter
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148 def nodeid(node):
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149 id = []
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150 if node.tag == 'Hsp':
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151 id.insert(0, node.Hsp_num.text)
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152 node = node.getparent().getparent()
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153 assert node.tag == 'Hit'
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154 if node.tag == 'Hit':
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155 id.insert(0, node.Hit_num.text)
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156 node = node.getparent().getparent()
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157 assert node.tag == 'Iteration'
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158 if node.tag == 'Iteration':
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159 id.insert(0, node['Iteration_iter-num'].text)
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160 return '-'.join(id)
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161 raise ValueError("The nodeid filter can only be applied to Hsp, Hit or Iteration nodes in a BlastXML document")
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162
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163
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164 @filter
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165 def asframe(frame):
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166 if frame == 1:
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167 return 'Plus'
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168 elif frame == -1:
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169 return 'Minus'
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170 raise Exception("frame should be either +1 or -1")
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171
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172 # def genelink(hit, type='genbank', hsp=None):
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173 # if not isinstance(hit, six.string_types):
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174 # hit = hitid(hit)
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175 # link = "http://www.ncbi.nlm.nih.gov/nucleotide/{0}?report={1}&log$=nuclalign".format(hit, type)
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176 # if hsp != None:
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177 # link += "&from={0}&to={1}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
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178 # return link
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179
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180
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181 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139
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182 # I've removed the html escapes, since html escaping is already being performed by the template engine.
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183
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184 # The r'\u0027' syntax doesn't work the way we need to in python 2.6 with unicode_literals
16
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185 _base_js_escapes = (
74
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186 ('\\', '\\u005C'),
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187 ('\'', '\\u0027'),
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188 ('"', '\\u0022'),
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189 # ('>', '\\u003E'),
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190 # ('<', '\\u003C'),
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191 # ('&', '\\u0026'),
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192 # ('=', '\\u003D'),
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193 # ('-', '\\u002D'),
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194 # (';', '\\u003B'),
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195 (u'\u2028', '\\u2028'),
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196 (u'\u2029', '\\u2029')
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197 )
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198
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199 # Escape every ASCII character with a value less than 32. This is
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200 # needed a.o. to prevent html parsers from jumping out of javascript
16
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201 # parsing mode.
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202 _js_escapes = (_base_js_escapes +
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203 tuple(('%c' % z, '\\u%04X' % z) for z in range(32)))
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204
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205 @filter
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206 def js_string_escape(value):
72
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207 """
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208 Javascript string literal escape. Note that this only escapes data
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209 for embedding within javascript string literals, not in general
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210 javascript snippets.
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211 """
16
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212
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213 value = str(value)
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214
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215 for bad, good in _js_escapes:
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216 value = value.replace(bad, good)
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diff changeset
217
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218 return value
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parents:
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219
19
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220 @filter
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221 def hits(result):
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222 # sort hits by longest hotspot first
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223 return sorted(result.Iteration_hits.findall('Hit'),
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diff changeset
224 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp),
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225 reverse=True)
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226
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227
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228
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229 class BlastVisualize:
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230
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231 colors = ('black', 'blue', 'green', 'magenta', 'red')
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232
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233 max_scale_labels = 10
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234
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235 def __init__(self, input, templatedir, templatename, genelinks={}):
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236 self.input = input
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237 self.templatename = templatename
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238 self.genelinks = genelinks
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239
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240 self.blast = objectify.parse(self.input).getroot()
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241 self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
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242 self.environment = jinja2.Environment(loader=self.loader,
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243 lstrip_blocks=True, trim_blocks=True, autoescape=True)
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244
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245 self._addfilters(self.environment)
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246
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247
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248 def _addfilters(self, environment):
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249 for filtername, funcname in _filters.items():
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diff changeset
250 try:
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251 environment.filters[filtername] = getattr(self, funcname)
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252 except AttributeError:
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diff changeset
253 try:
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254 environment.filters[filtername] = globals()[funcname]
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255 except KeyError:
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256 environment.filters[filtername] = getattr(builtins, funcname)
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257
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258 def render(self, output):
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259 template = self.environment.get_template(self.templatename)
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260
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261 params = (('Query ID', self.blast["BlastOutput_query-ID"]),
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262 ('Query definition', self.blast["BlastOutput_query-def"]),
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263 ('Query length', self.blast["BlastOutput_query-len"]),
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264 ('Program', self.blast.BlastOutput_version),
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265 ('Database', self.blast.BlastOutput_db),
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266 )
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267
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268 result = template.render(blast=self.blast,
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269 iterations=self.blast.BlastOutput_iterations.Iteration,
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270 colors=self.colors,
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271 params=params)
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diff changeset
272 if six.PY2:
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273 result = result.encode('utf-8')
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274 output.write(result)
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275
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276 @filter
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277 def match_colors(self, result):
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278 """
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279 An iterator that yields lists of length-color pairs.
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280 """
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281
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282 query_length = blastxml_len(result)
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283
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284 percent_multiplier = 100 / query_length
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285
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diff changeset
286 for hit in hits(result):
12
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parents: 11
diff changeset
287 # sort hotspots from short to long, so we can overwrite index colors of
a459c754cdb5 add links, refactor, proper commandline arguments
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parents: 11
diff changeset
288 # short matches with those of long ones.
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
289 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp))
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
290 table = bytearray([255]) * query_length
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
291 for hsp in hotspots:
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
292 frm = hsp['Hsp_query-from'] - 1
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
293 to = int(hsp['Hsp_query-to'])
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
294 table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm)
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
295
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
296 matches = []
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
297 last = table[0]
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
298 count = 0
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
299 for i in range(query_length):
12
a459c754cdb5 add links, refactor, proper commandline arguments
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parents: 11
diff changeset
300 if table[i] == last:
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
301 count += 1
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
302 continue
16
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
303 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
304 last = table[i]
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
305 count = 1
16
db7e4ee3be03 fix validation, reindent
Jan Kanis <jan.code@jankanis.nl>
parents: 15
diff changeset
306 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
12
a459c754cdb5 add links, refactor, proper commandline arguments
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parents: 11
diff changeset
307
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
308 yield dict(colors=matches, hit=hit, defline=firsttitle(hit))
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
309
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
310 @filter
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
311 def queryscale(self, result):
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
312 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
313 skip = math.ceil(query_length / self.max_scale_labels)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
314 percent_multiplier = 100 / query_length
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
315 for i in range(1, query_length+1):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
316 if i % skip == 0:
23
6995a6f34f3f fix sectioning, add footer
Jan Kanis <jan.code@jankanis.nl>
parents: 22
diff changeset
317 yield dict(label = i, width = skip * percent_multiplier)
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
318 if query_length % skip != 0:
20
53cd304c5f26 Add index for multiple results; fix layout of query ruler for edge case
Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
319 yield dict(label = query_length,
23
6995a6f34f3f fix sectioning, add footer
Jan Kanis <jan.code@jankanis.nl>
parents: 22
diff changeset
320 width = (query_length % skip) * percent_multiplier)
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
321
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
322 @filter
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
323 def hit_info(self, result):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
324
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
325 query_length = blastxml_len(result)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
326
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
327 for hit in hits(result):
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
328 hsps = hit.Hit_hsps.Hsp
7
9e7927673089 intermediate commit before converting some tables to divs
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
329
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
330 cover = [False] * query_length
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
331 for hsp in hsps:
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 18
diff changeset
332 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp))
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
333 cover_count = cover.count(True)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
334
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
335 def hsp_val(path):
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
336 return (float(hsp[path]) for hsp in hsps)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
337
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
338 yield dict(hit = hit,
75
4d2c25baf5a3 Fix rounding errors
Jan Kanis <jan.code@jankanis.nl>
parents: 74
diff changeset
339 title = firsttitle(hit),
73
67b1a319c6dc First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents: 72
diff changeset
340 maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))),
67b1a319c6dc First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents: 72
diff changeset
341 totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
67b1a319c6dc First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents: 72
diff changeset
342 cover = "{0:.0%}".format(cover_count / query_length),
67b1a319c6dc First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents: 72
diff changeset
343 e_value = "{0:.4g}".format(min(hsp_val('Hsp_evalue'))),
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
344 # FIXME: is this the correct formula vv?
78
c0804e6443c6 comment
Jan Kanis <jan.code@jankanis.nl>
parents: 76
diff changeset
345 # float(...) because non-flooring division doesn't work with lxml elements in python 2.6
95
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
346 ident = "{0:.0%}".format(float(min(float(hsp.Hsp_identity) / blastxml_len(hsp) for hsp in hsps))))
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
347
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
348 @filter
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
349 def genelink(self, hit, text=None, clas=None, display_nolink=True):
96
02b795b784e1 fix bug; add comments
Jan Kanis <jan.code@jankanis.nl>
parents: 95
diff changeset
350 """Create a html link from a hit node to a configured gene bank webpage.
02b795b784e1 fix bug; add comments
Jan Kanis <jan.code@jankanis.nl>
parents: 95
diff changeset
351 text: The text of the link, defaults to the hit_id
02b795b784e1 fix bug; add comments
Jan Kanis <jan.code@jankanis.nl>
parents: 95
diff changeset
352 clas: extra css classes that will be added to the <a> element
02b795b784e1 fix bug; add comments
Jan Kanis <jan.code@jankanis.nl>
parents: 95
diff changeset
353 display_nolink: boolean, if false don't display anything if no link can be created. Default True.
02b795b784e1 fix bug; add comments
Jan Kanis <jan.code@jankanis.nl>
parents: 95
diff changeset
354 """
02b795b784e1 fix bug; add comments
Jan Kanis <jan.code@jankanis.nl>
parents: 95
diff changeset
355
95
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
356 if text is None:
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
357 text = hitid(hit)
96
02b795b784e1 fix bug; add comments
Jan Kanis <jan.code@jankanis.nl>
parents: 95
diff changeset
358
95
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
359 db = hit.getroottree().getroot().BlastOutput_db
96
02b795b784e1 fix bug; add comments
Jan Kanis <jan.code@jankanis.nl>
parents: 95
diff changeset
360
95
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
361 if isinstance(self.genelinks, six.string_types):
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
362 template = self.genelinks
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
363 else:
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
364 template = self.genelinks.get(db)
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
365 if template is None:
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
366 return text if display_nolink else ''
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
367 args = dict(id=hitid(hit).split('|'),
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
368 fullid=hitid(hit),
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
369 defline=str(hit.Hit_def).split('|'),
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
370 fulldefline=str(hit.Hit_def),
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
371 accession=str(hit.Hit_accession))
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
372 try:
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
373 link = template.format(**args)
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
374 except Exception as e:
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
375 warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e))
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
376 return text if display_nolink else ''
96
02b795b784e1 fix bug; add comments
Jan Kanis <jan.code@jankanis.nl>
parents: 95
diff changeset
377
99
8f02008a5f20 look at all blast*.loc files; python2.6 compat fix
Jan Kanis <jan.code@jankanis.nl>
parents: 98
diff changeset
378 classattr = 'class="{0}" '.format(jinja2.escape(clas)) if clas is not None else ''
8f02008a5f20 look at all blast*.loc files; python2.6 compat fix
Jan Kanis <jan.code@jankanis.nl>
parents: 98
diff changeset
379 return jinja2.Markup("<a {0}href=\"{1}\">{2}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text)))
95
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
380
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
381
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
382 def read_genelinks(dir):
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
383 links = {}
99
8f02008a5f20 look at all blast*.loc files; python2.6 compat fix
Jan Kanis <jan.code@jankanis.nl>
parents: 98
diff changeset
384 # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc.
101
5bfaa3ee1f27 better warning message
Jan Kanis <jan.code@jankanis.nl>
parents: 99
diff changeset
385 files = sorted(glob.glob(path.join(dir, 'blastdb*.loc')))
5bfaa3ee1f27 better warning message
Jan Kanis <jan.code@jankanis.nl>
parents: 99
diff changeset
386 # reversed, so blastdb.loc will take precedence
5bfaa3ee1f27 better warning message
Jan Kanis <jan.code@jankanis.nl>
parents: 99
diff changeset
387 for f in reversed(files):
95
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
388 try:
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
389 f = open(path.join(dir, f))
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
390 for l in f.readlines():
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
391 if l.strip().startswith('#'):
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
392 continue
98
e780606b7c25 test new command line parameters, fix small bug
Jan Kanis <jan.code@jankanis.nl>
parents: 96
diff changeset
393 line = l.rstrip('\n').split('\t')
95
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
394 try:
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
395 links[line[2]] = line[3]
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
396 except IndexError:
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
397 continue
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
398 f.close()
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
399 except OSError:
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
400 continue
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
401 if not links:
103
86bcf17f50ef improve warning messages
Jan Kanis <jan.code@jankanis.nl>
parents: 102
diff changeset
402 if not files:
86bcf17f50ef improve warning messages
Jan Kanis <jan.code@jankanis.nl>
parents: 102
diff changeset
403 warnings.warn("No gene bank link templates found (no blastdb*.loc files found in {0})".format(dir))
86bcf17f50ef improve warning messages
Jan Kanis <jan.code@jankanis.nl>
parents: 102
diff changeset
404 else:
86bcf17f50ef improve warning messages
Jan Kanis <jan.code@jankanis.nl>
parents: 102
diff changeset
405 warnings.warn("No gene bank link templates found in {0}".format(', '.join(files)))
95
4378d11f0ed7 implement configurable gene bank links
Jan Kanis <jan.code@jankanis.nl>
parents: 79
diff changeset
406 return links
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
407
27
4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
Jan Kanis <jan.code@jankanis.nl>
parents: 24
diff changeset
408
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
409 def main():
27
4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
Jan Kanis <jan.code@jankanis.nl>
parents: 24
diff changeset
410 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')
73
67b1a319c6dc First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents: 72
diff changeset
411
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
412 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
73
67b1a319c6dc First go at 2.6 compatibility
Jan Kanis <jan.code@jankanis.nl>
parents: 72
diff changeset
413 usage="{0} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
414 input_group = parser.add_mutually_exclusive_group(required=True)
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
415 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
416 help='The input Blast XML file, same as -i/--input')
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
417 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'),
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
418 help='The input Blast XML file')
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
419 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
12
a459c754cdb5 add links, refactor, proper commandline arguments
Jan Kanis <jan.code@jankanis.nl>
parents: 11
diff changeset
420 help='The output html file')
18
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
421 # We just want the file name here, so jinja can open the file
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
422 # itself. But it is easier to just use a FileType so argparse can
4434ffab721a add a parameter for the template
Jan Kanis <jan.code@jankanis.nl>
parents: 16
diff changeset
423 # handle the errors. This introduces a small race condition when
4434ffab721a add a parameter for the template
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424 # jinja later tries to re-open the template file, but we don't
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425 # care too much.
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426 parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template,
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427 help='The template file to use. Defaults to blast_html.html.jinja')
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428
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429 dblink_group = parser.add_mutually_exclusive_group()
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430 dblink_group.add_argument('--genelink-template', default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
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431 help="""A link template to link hits to a gene bank webpage. The template string is a
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432 Python format string. It can contain the following replacement elements: {id[N]}, {fullid},
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433 {defline[N]}, {fulldefline}, {accession}, where N is a number. id[N] and defline[N] will be
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434 replaced by the Nth element of the id or defline, where '|' is the field separator.
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435
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436 The default is 'http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign',
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437 which is a link to the NCBI nucleotide database.""")
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438
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439 dblink_group.add_argument('--db-config-dir',
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440 help="""The directory where databases are configured in blastdb*.loc files. These files
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441 are consulted for creating a gene bank link. The files should be tab-separated tables (with lines
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442 starting with '#' ignored), where the third field of a line should be a database path and the fourth
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443 a genebank link template conforming to the --genelink-template option syntax.
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444
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445 This option is incompatible with --genelink-template.""")
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446
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447 args = parser.parse_args()
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448 if args.input == None:
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449 args.input = args.positional_arg
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450 if args.input == None:
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451 parser.error('no input specified')
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452
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453 templatedir, templatename = path.split(args.template.name)
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454 args.template.close()
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455 if not templatedir:
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456 templatedir = '.'
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457
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458 if args.db_config_dir is None:
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459 genelinks = args.genelink_template
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460 elif not path.isdir(args.db_config_dir):
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461 parser.error('db-config-dir does not exist or is not a directory')
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462 else:
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463 genelinks = read_genelinks(args.db_config_dir)
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464
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465 b = BlastVisualize(args.input, templatedir, templatename, genelinks)
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466 b.render(args.output)
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467
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468
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469 if __name__ == '__main__':
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470 main()
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471