Mercurial > repos > jankanis > blast2html
annotate blast2html.py @ 91:20639b08d781
fix LD_LIBRARY_PATH
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Tue, 24 Jun 2014 17:59:12 +0200 |
| parents | 9fb1a7d67317 |
| children | 4378d11f0ed7 |
| rev | line source |
|---|---|
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1 #!/usr/bin/env python3 |
| 50 | 2 # -*- coding: utf-8 -*- |
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3 |
| 75 | 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 |
| 72 | 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 |
| 50 | 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 |
| 75 | 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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21 |
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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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35 |
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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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70 |
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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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75 |
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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""" |
| 71 | 106 |
| 107 # line break length | |
| 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']) |
| 69 | 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']) |
| 69 | 115 hframe = int(hsp['Hsp_hit-frame']) |
| 71 | 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 |
| 69 | 120 |
| 71 | 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)) |
| 69 | 123 qframe = -1 if qframe < 0 else 1 |
| 71 | 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)) |
| 69 | 126 hframe = -1 if hframe < 0 else 1 |
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127 |
| 69 | 128 def split(txt): |
| 71 | 129 return [txt[i:i+linewidth] for i in range(0, len(txt), linewidth)] |
| 69 | 130 |
| 71 | 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 |
| 69 | 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))) |
| 69 | 141 if hfrom+(len(hseq)-1)*hframe != hto: |
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142 warnings.warn("Error in BlastXML input: Hsp node {0} hseq length mismatch: from {1} to {2} length {3}".format( |
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143 nodeid(hsp), hfrom, hto, len(hseq))) |
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144 |
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145 |
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146 |
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147 @filter('len') |
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148 def blastxml_len(node): |
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149 if node.tag == 'Hsp': |
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150 return int(node['Hsp_align-len']) |
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151 elif node.tag == 'Iteration': |
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152 return int(node['Iteration_query-len']) |
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153 raise Exception("Unknown XML node type: "+node.tag) |
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154 |
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155 @filter |
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156 def nodeid(node): |
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157 id = [] |
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158 if node.tag == 'Hsp': |
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159 id.insert(0, node.Hsp_num.text) |
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160 node = node.getparent().getparent() |
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161 assert node.tag == 'Hit' |
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162 if node.tag == 'Hit': |
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163 id.insert(0, node.Hit_num.text) |
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164 node = node.getparent().getparent() |
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165 assert node.tag == 'Iteration' |
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166 if node.tag == 'Iteration': |
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167 id.insert(0, node['Iteration_iter-num'].text) |
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168 return '-'.join(id) |
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169 raise ValueError("The nodeid filter can only be applied to Hsp, Hit or Iteration nodes in a BlastXML document") |
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170 |
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171 |
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172 @filter |
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173 def asframe(frame): |
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174 if frame == 1: |
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175 return 'Plus' |
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176 elif frame == -1: |
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177 return 'Minus' |
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178 raise Exception("frame should be either +1 or -1") |
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179 |
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180 def genelink(hit, type='genbank', hsp=None): |
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181 if not isinstance(hit, six.string_types): |
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182 hit = hitid(hit) |
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183 link = "http://www.ncbi.nlm.nih.gov/nucleotide/{0}?report={1}&log$=nuclalign".format(hit, type) |
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184 if hsp != None: |
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185 link += "&from={0}&to={1}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to']) |
| 16 | 186 return link |
| 187 | |
| 188 | |
| 189 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139 | |
| 190 # I've removed the html escapes, since html escaping is already being performed by the template engine. | |
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191 |
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192 # The r'\u0027' syntax doesn't work the way we need to in python 2.6 with unicode_literals |
| 16 | 193 _base_js_escapes = ( |
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194 ('\\', '\\u005C'), |
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195 ('\'', '\\u0027'), |
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196 ('"', '\\u0022'), |
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197 # ('>', '\\u003E'), |
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198 # ('<', '\\u003C'), |
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199 # ('&', '\\u0026'), |
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200 # ('=', '\\u003D'), |
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201 # ('-', '\\u002D'), |
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202 # (';', '\\u003B'), |
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203 (u'\u2028', '\\u2028'), |
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204 (u'\u2029', '\\u2029') |
| 16 | 205 ) |
| 206 | |
| 207 # Escape every ASCII character with a value less than 32. This is | |
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208 # needed a.o. to prevent html parsers from jumping out of javascript |
| 16 | 209 # parsing mode. |
| 210 _js_escapes = (_base_js_escapes + | |
| 211 tuple(('%c' % z, '\\u%04X' % z) for z in range(32))) | |
| 212 | |
| 213 @filter | |
| 214 def js_string_escape(value): | |
| 72 | 215 """ |
| 216 Javascript string literal escape. Note that this only escapes data | |
| 217 for embedding within javascript string literals, not in general | |
| 218 javascript snippets. | |
| 219 """ | |
| 16 | 220 |
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221 value = six.text_type(value) |
| 16 | 222 |
| 223 for bad, good in _js_escapes: | |
| 224 value = value.replace(bad, good) | |
| 225 | |
| 226 return value | |
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227 |
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228 @filter |
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229 def hits(result): |
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230 # sort hits by longest hotspot first |
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231 return sorted(result.Iteration_hits.findall('Hit'), |
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232 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp), |
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233 reverse=True) |
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234 |
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235 |
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236 |
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237 class BlastVisualize: |
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238 |
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239 colors = ('black', 'blue', 'green', 'magenta', 'red') |
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240 |
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241 max_scale_labels = 10 |
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242 |
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243 def __init__(self, input, templatedir, templatename): |
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244 self.input = input |
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245 self.templatename = templatename |
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246 |
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247 self.blast = objectify.parse(self.input).getroot() |
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248 self.loader = jinja2.FileSystemLoader(searchpath=templatedir) |
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249 self.environment = jinja2.Environment(loader=self.loader, |
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250 lstrip_blocks=True, trim_blocks=True, autoescape=True) |
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251 |
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252 self._addfilters(self.environment) |
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253 |
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254 |
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255 def _addfilters(self, environment): |
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256 for filtername, funcname in _filters.items(): |
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257 try: |
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258 environment.filters[filtername] = getattr(self, funcname) |
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259 except AttributeError: |
| 75 | 260 try: |
| 261 environment.filters[filtername] = globals()[funcname] | |
| 262 except KeyError: | |
| 263 environment.filters[filtername] = getattr(builtins, funcname) | |
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264 |
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265 def render(self, output): |
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266 template = self.environment.get_template(self.templatename) |
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267 |
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268 params = (('Query ID', self.blast["BlastOutput_query-ID"]), |
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269 ('Query definition', self.blast["BlastOutput_query-def"]), |
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270 ('Query length', self.blast["BlastOutput_query-len"]), |
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271 ('Program', self.blast.BlastOutput_version), |
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272 ('Database', self.blast.BlastOutput_db), |
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273 ) |
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274 |
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275 result = template.render(blast=self.blast, |
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276 iterations=self.blast.BlastOutput_iterations.Iteration, |
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277 colors=self.colors, |
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278 genelink=genelink, |
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279 params=params) |
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280 if six.PY2: |
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281 result = result.encode('utf-8') |
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282 output.write(result) |
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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 |
| 16 | 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 |
| 16 | 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: |
| 23 | 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, |
| 23 | 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, |
| 75 | 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? |
| 78 | 353 # float(...) because non-flooring division doesn't work with lxml elements in python 2.6 |
| 75 | 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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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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384 templatedir, templatename = path.split(args.template.name) |
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385 args.template.close() |
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386 if not templatedir: |
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387 templatedir = '.' |
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388 |
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389 b = BlastVisualize(args.input, templatedir, templatename) |
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390 b.render(args.output) |
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391 |
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392 |
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393 if __name__ == '__main__': |
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394 main() |
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395 |