Mercurial > repos > jankanis > blast2html
annotate blast2html.py @ 69:0c4ac210068b
handle reverse matches
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Wed, 18 Jun 2014 14:12:00 +0200 |
| parents | fa8a93bdefd7 |
| children | 371cd585e459 |
| rev | line source |
|---|---|
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1 #!/usr/bin/env python3 |
| 50 | 2 # -*- coding: utf-8 -*- |
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3 |
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4 # Copyright The Hyve B.V. 2014 |
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5 # License: GPL version 3 or higher |
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6 |
| 50 | 7 from __future__ import unicode_literals |
| 8 | |
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9 import sys |
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10 import math |
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11 import warnings |
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12 from os import path |
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13 from itertools import repeat |
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14 import argparse |
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15 from lxml import objectify |
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16 import jinja2 |
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17 |
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18 |
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19 |
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20 _filters = {} |
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21 def filter(func_or_name): |
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22 "Decorator to register a function as filter in the current jinja environment" |
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23 if isinstance(func_or_name, str): |
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24 def inner(func): |
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25 _filters[func_or_name] = func.__name__ |
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26 return func |
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27 return inner |
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28 else: |
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29 _filters[func_or_name.__name__] = func_or_name.__name__ |
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30 return func_or_name |
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31 |
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32 |
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33 def color_idx(length): |
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34 if length < 40: |
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35 return 0 |
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36 elif length < 50: |
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37 return 1 |
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38 elif length < 80: |
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39 return 2 |
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40 elif length < 200: |
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41 return 3 |
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42 return 4 |
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43 |
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44 @filter |
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45 def fmt(val, fmt): |
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46 return format(float(val), fmt) |
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47 |
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48 @filter |
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49 def firsttitle(hit): |
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50 return hit.Hit_def.text.split('>')[0] |
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51 |
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52 @filter |
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53 def othertitles(hit): |
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54 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles.""" |
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55 id_titles = hit.Hit_def.text.split('>') |
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56 |
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57 titles = [] |
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58 for t in id_titles[1:]: |
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59 fullid, title = t.split(' ', 1) |
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60 hitid, id = fullid.split('|', 2)[1:3] |
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61 titles.append(dict(id = id, |
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62 hitid = hitid, |
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63 fullid = fullid, |
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64 title = title)) |
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65 return titles |
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66 |
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67 @filter |
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68 def hitid(hit): |
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69 hitid = hit.Hit_id.text |
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70 s = hitid.split('|', 2) |
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71 if len(s) >= 2: |
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72 return s[1] |
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73 return hitid |
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74 |
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75 @filter |
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76 def seqid(hit): |
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77 hitid = hit.Hit_id.text |
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78 s = hitid.split('|', 2) |
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79 if len(s) >= 3: |
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80 return s[2] |
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81 return hitid |
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82 |
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83 |
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84 @filter |
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85 def alignment_pre(hsp): |
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86 """Create the preformatted alignment blocks""" |
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87 |
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88 step = 60 |
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89 |
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90 qfrom = int(hsp['Hsp_query-from']) |
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91 qto = int(hsp['Hsp_query-to']) |
| 69 | 92 qframe = int(hsp['Hsp_query-frame']) |
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93 hfrom = int(hsp['Hsp_hit-from']) |
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94 hto = int(hsp['Hsp_hit-to']) |
| 69 | 95 hframe = int(hsp['Hsp_hit-frame']) |
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96 qseq = hsp.Hsp_qseq.text |
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97 midline = hsp.Hsp_midline.text |
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98 hseq = hsp.Hsp_hseq.text |
| 69 | 99 |
| 100 if not qframe in [1, -1]: | |
| 101 warnings.warn("Error in BlastXML input: Hsp node {} has a Hsp_query-frame of {}".format(nodeid(hsp), qframe)) | |
| 102 qframe = -1 if qframe < 0 else 1 | |
| 103 if not hframe in [1, -1]: | |
| 104 warnings.warn("Error in BlastXML input: Hsp node {} has a Hsp_hit-frame of {}".format(nodeid(hsp), hframe)) | |
| 105 hframe = -1 if hframe < 0 else 1 | |
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106 |
| 69 | 107 def split(txt): |
| 108 return [txt[i:i+step] for i in range(0, len(txt), step)] | |
| 109 | |
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110 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), step)): |
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111 yield ( |
| 69 | 112 "Query {:>7} {} {}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) + |
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113 " {:7} {}\n".format('', mid) + |
| 69 | 114 "Subject{:>7} {} {}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe) |
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115 ) |
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116 |
| 69 | 117 if qfrom+(len(qseq)-1)*qframe != qto: |
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118 warnings.warn("Error in BlastXML input: Hsp node {} qseq length mismatch: from {} to {} length {}".format( |
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119 nodeid(hsp), qfrom, qto, len(qseq))) |
| 69 | 120 if hfrom+(len(hseq)-1)*hframe != hto: |
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121 warnings.warn("Error in BlastXML input: Hsp node {} hseq length mismatch: from {} to {} length {}".format( |
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122 nodeid(hsp), hfrom, hto, len(hseq))) |
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123 |
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124 |
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125 |
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126 @filter('len') |
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127 def blastxml_len(node): |
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128 if node.tag == 'Hsp': |
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129 return int(node['Hsp_align-len']) |
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130 elif node.tag == 'Iteration': |
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131 return int(node['Iteration_query-len']) |
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132 raise Exception("Unknown XML node type: "+node.tag) |
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133 |
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134 @filter |
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135 def nodeid(node): |
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136 id = [] |
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137 if node.tag == 'Hsp': |
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138 id.insert(0, node.Hsp_num.text) |
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139 node = node.getparent().getparent() |
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140 assert node.tag == 'Hit' |
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141 if node.tag == 'Hit': |
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142 id.insert(0, node.Hit_num.text) |
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143 node = node.getparent().getparent() |
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144 assert node.tag == 'Iteration' |
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145 if node.tag == 'Iteration': |
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146 id.insert(0, node['Iteration_iter-num'].text) |
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147 return '-'.join(id) |
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148 raise ValueError("The nodeid filter can only be applied to Hsp, Hit or Iteration nodes in a BlastXML document") |
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149 |
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150 |
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151 @filter |
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152 def asframe(frame): |
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153 if frame == 1: |
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154 return 'Plus' |
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155 elif frame == -1: |
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156 return 'Minus' |
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157 raise Exception("frame should be either +1 or -1") |
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158 |
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159 def genelink(hit, type='genbank', hsp=None): |
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160 if not isinstance(hit, str): |
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161 hit = hitid(hit) |
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162 link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type) |
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163 if hsp != None: |
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164 link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to']) |
| 16 | 165 return link |
| 166 | |
| 167 | |
| 168 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139 | |
| 169 # I've removed the html escapes, since html escaping is already being performed by the template engine. | |
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170 |
| 16 | 171 _base_js_escapes = ( |
| 172 ('\\', r'\u005C'), | |
| 173 ('\'', r'\u0027'), | |
| 174 ('"', r'\u0022'), | |
| 175 # ('>', r'\u003E'), | |
| 176 # ('<', r'\u003C'), | |
| 177 # ('&', r'\u0026'), | |
| 178 # ('=', r'\u003D'), | |
| 179 # ('-', r'\u002D'), | |
| 180 # (';', r'\u003B'), | |
| 181 # (u'\u2028', r'\u2028'), | |
| 182 # (u'\u2029', r'\u2029') | |
| 183 ) | |
| 184 | |
| 185 # Escape every ASCII character with a value less than 32. This is | |
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186 # needed a.o. to prevent html parsers from jumping out of javascript |
| 16 | 187 # parsing mode. |
| 188 _js_escapes = (_base_js_escapes + | |
| 189 tuple(('%c' % z, '\\u%04X' % z) for z in range(32))) | |
| 190 | |
| 191 @filter | |
| 192 def js_string_escape(value): | |
| 193 """Escape javascript string literal escapes. Note that this only works | |
| 194 within javascript string literals, not in general javascript | |
| 195 snippets.""" | |
| 196 | |
| 197 value = str(value) | |
| 198 | |
| 199 for bad, good in _js_escapes: | |
| 200 value = value.replace(bad, good) | |
| 201 | |
| 202 return value | |
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203 |
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204 @filter |
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205 def hits(result): |
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206 # sort hits by longest hotspot first |
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207 return sorted(result.Iteration_hits.findall('Hit'), |
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208 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp), |
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209 reverse=True) |
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210 |
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211 |
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212 |
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213 class BlastVisualize: |
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214 |
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215 colors = ('black', 'blue', 'green', 'magenta', 'red') |
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216 |
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217 max_scale_labels = 10 |
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218 |
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219 def __init__(self, input, templatedir, templatename): |
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220 self.input = input |
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221 self.templatename = templatename |
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222 |
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223 self.blast = objectify.parse(self.input).getroot() |
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224 self.loader = jinja2.FileSystemLoader(searchpath=templatedir) |
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225 self.environment = jinja2.Environment(loader=self.loader, |
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226 lstrip_blocks=True, trim_blocks=True, autoescape=True) |
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227 |
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228 self._addfilters(self.environment) |
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229 |
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230 |
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231 def _addfilters(self, environment): |
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232 for filtername, funcname in _filters.items(): |
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233 try: |
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234 environment.filters[filtername] = getattr(self, funcname) |
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235 except AttributeError: |
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236 environment.filters[filtername] = globals()[funcname] |
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237 |
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238 def render(self, output): |
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239 template = self.environment.get_template(self.templatename) |
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240 |
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241 params = (('Query ID', self.blast["BlastOutput_query-ID"]), |
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242 ('Query definition', self.blast["BlastOutput_query-def"]), |
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243 ('Query length', self.blast["BlastOutput_query-len"]), |
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244 ('Program', self.blast.BlastOutput_version), |
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245 ('Database', self.blast.BlastOutput_db), |
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246 ) |
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247 |
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248 output.write(template.render(blast=self.blast, |
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249 iterations=self.blast.BlastOutput_iterations.Iteration, |
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250 colors=self.colors, |
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251 # match_colors=self.match_colors(), |
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252 # hit_info=self.hit_info(), |
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253 genelink=genelink, |
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254 params=params)) |
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255 |
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256 @filter |
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257 def match_colors(self, result): |
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258 """ |
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259 An iterator that yields lists of length-color pairs. |
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260 """ |
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261 |
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262 query_length = blastxml_len(result) |
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263 |
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264 percent_multiplier = 100 / query_length |
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265 |
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266 for hit in hits(result): |
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267 # sort hotspots from short to long, so we can overwrite index colors of |
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268 # short matches with those of long ones. |
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269 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp)) |
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270 table = bytearray([255]) * query_length |
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271 for hsp in hotspots: |
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272 frm = hsp['Hsp_query-from'] - 1 |
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273 to = int(hsp['Hsp_query-to']) |
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274 table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm) |
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275 |
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276 matches = [] |
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277 last = table[0] |
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278 count = 0 |
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279 for i in range(query_length): |
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280 if table[i] == last: |
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281 count += 1 |
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282 continue |
| 16 | 283 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) |
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284 last = table[i] |
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285 count = 1 |
| 16 | 286 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) |
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287 |
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288 yield dict(colors=matches, hit=hit, defline=firsttitle(hit)) |
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289 |
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290 @filter |
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291 def queryscale(self, result): |
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292 query_length = blastxml_len(result) |
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293 skip = math.ceil(query_length / self.max_scale_labels) |
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294 percent_multiplier = 100 / query_length |
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295 for i in range(1, query_length+1): |
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296 if i % skip == 0: |
| 23 | 297 yield dict(label = i, width = skip * percent_multiplier) |
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298 if query_length % skip != 0: |
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299 yield dict(label = query_length, |
| 23 | 300 width = (query_length % skip) * percent_multiplier) |
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301 |
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302 @filter |
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303 def hit_info(self, result): |
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304 |
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305 query_length = blastxml_len(result) |
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306 |
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307 for hit in hits(result): |
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308 hsps = hit.Hit_hsps.Hsp |
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309 |
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310 cover = [False] * query_length |
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311 for hsp in hsps: |
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312 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp)) |
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313 cover_count = cover.count(True) |
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314 |
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315 def hsp_val(path): |
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316 return (float(hsp[path]) for hsp in hsps) |
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317 |
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318 yield dict(hit = hit, |
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319 title = firsttitle(hit), |
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320 maxscore = "{:.1f}".format(max(hsp_val('Hsp_bit-score'))), |
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321 totalscore = "{:.1f}".format(sum(hsp_val('Hsp_bit-score'))), |
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322 cover = "{:.0%}".format(cover_count / query_length), |
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323 e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))), |
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324 # FIXME: is this the correct formula vv? |
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325 ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))), |
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326 accession = hit.Hit_accession) |
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327 |
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328 |
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329 def main(): |
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330 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja') |
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331 |
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332 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page", |
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333 usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0])) |
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334 input_group = parser.add_mutually_exclusive_group(required=True) |
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335 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'), |
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336 help='The input Blast XML file, same as -i/--input') |
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337 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), |
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338 help='The input Blast XML file') |
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339 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout, |
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340 help='The output html file') |
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341 # We just want the file name here, so jinja can open the file |
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342 # itself. But it is easier to just use a FileType so argparse can |
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343 # handle the errors. This introduces a small race condition when |
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344 # jinja later tries to re-open the template file, but we don't |
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345 # care too much. |
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346 parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template, |
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347 help='The template file to use. Defaults to blast_html.html.jinja') |
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348 |
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349 args = parser.parse_args() |
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350 if args.input == None: |
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351 args.input = args.positional_arg |
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352 if args.input == None: |
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353 parser.error('no input specified') |
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354 |
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355 templatedir, templatename = path.split(args.template.name) |
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356 args.template.close() |
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357 if not templatedir: |
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358 templatedir = '.' |
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359 |
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360 b = BlastVisualize(args.input, templatedir, templatename) |
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361 b.render(args.output) |
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362 |
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363 |
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364 if __name__ == '__main__': |
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365 main() |
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366 |