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| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Thu, 23 Jul 2015 12:24:40 +0200 |
| parents | 0fa962dd83b4 |
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| 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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| 126 | 6 # Copyright The Hyve B.V. 2014-2015 |
| 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 |
| 104 | 14 import six, codecs, io |
| 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 from collections import defaultdict, namedtuple |
| 120 | 19 from array import array |
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20 import glob |
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21 import argparse |
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22 from lxml import objectify |
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23 import jinja2 |
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24 |
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25 builtin_str = str |
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26 str = six.text_type |
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27 |
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28 |
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29 |
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30 _filters = dict(float='float') |
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31 def filter(func_or_name): |
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32 "Decorator to register a function as filter in the current jinja environment" |
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33 if isinstance(func_or_name, six.string_types): |
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34 def inner(func): |
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35 _filters[func_or_name] = func.__name__ |
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36 return func |
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37 return inner |
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38 else: |
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39 _filters[func_or_name.__name__] = func_or_name.__name__ |
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40 return func_or_name |
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41 |
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42 |
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43 def color_idx(length): |
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44 if length < 40: |
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45 return 0 |
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46 elif length < 50: |
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47 return 1 |
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48 elif length < 80: |
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49 return 2 |
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50 elif length < 200: |
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51 return 3 |
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52 return 4 |
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53 |
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54 @filter |
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55 def fmt(val, fmt): |
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56 return format(float(val), fmt) |
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57 |
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58 @filter |
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59 def numfmt(val): |
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60 """Format numbers in decimal notation, but without excessive trailing 0's. |
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61 Default python float formatting will use scientific notation for some values, |
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62 or append trailing zeros with the 'f' format type, and the number of digits differs |
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63 between python 2 and 3.""" |
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64 fpart, ipart = math.modf(val) |
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65 if fpart == 0: |
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66 return str(int(val)) |
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67 # round to 10 to get identical representations in python 2 and 3 |
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68 s = format(round(val, 10), '.10f').rstrip('0') |
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69 if s[-1] == '.': |
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70 s += '0' |
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71 return s |
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72 |
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73 @filter |
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74 def firsttitle(hit): |
| 96 | 75 return str(hit.Hit_def).split('>')[0] |
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76 |
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77 @filter |
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78 def othertitles(hit): |
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79 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles.""" |
| 96 | 80 id_titles = str(hit.Hit_def).split('>') |
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81 |
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82 titles = [] |
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83 for t in id_titles[1:]: |
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84 id, title = t.split(' ', 1) |
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85 titles.append(argparse.Namespace(Hit_id = id, |
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86 Hit_def = title, |
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87 Hit_accession = '', |
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88 getroottree = hit.getroottree)) |
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89 return titles |
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90 |
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91 @filter |
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92 def hitid(hit): |
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93 return str(hit.Hit_id) |
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94 |
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95 |
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96 @filter |
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97 def alignment_pre(hsp): |
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98 """Create the preformatted alignment blocks""" |
| 71 | 99 |
| 100 # line break length | |
| 101 linewidth = 60 | |
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102 |
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103 qfrom = int(hsp['Hsp_query-from']) |
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104 qto = int(hsp['Hsp_query-to']) |
| 69 | 105 qframe = int(hsp['Hsp_query-frame']) |
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106 hfrom = int(hsp['Hsp_hit-from']) |
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107 hto = int(hsp['Hsp_hit-to']) |
| 69 | 108 hframe = int(hsp['Hsp_hit-frame']) |
| 71 | 109 |
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110 qseq = hsp.Hsp_qseq.text |
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111 midline = hsp.Hsp_midline.text |
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112 hseq = hsp.Hsp_hseq.text |
| 69 | 113 |
| 71 | 114 if not qframe in (1, -1): |
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115 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 | 116 qframe = -1 if qframe < 0 else 1 |
| 71 | 117 if not hframe in (1, -1): |
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118 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 | 119 hframe = -1 if hframe < 0 else 1 |
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120 |
| 69 | 121 def split(txt): |
| 71 | 122 return [txt[i:i+linewidth] for i in range(0, len(txt), linewidth)] |
| 69 | 123 |
| 71 | 124 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), linewidth)): |
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125 yield ( |
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126 "Query {0:>7} {1} {2}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) + |
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127 " {0:7} {1}\n".format('', mid) + |
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128 "Subject{0:>7} {1} {2}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe) |
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129 ) |
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130 |
| 69 | 131 if qfrom+(len(qseq)-1)*qframe != qto: |
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132 warnings.warn("Error in BlastXML input: Hsp node {0} qseq length mismatch: from {1} to {2} length {3}".format( |
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133 nodeid(hsp), qfrom, qto, len(qseq))) |
| 69 | 134 if hfrom+(len(hseq)-1)*hframe != hto: |
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135 warnings.warn("Error in BlastXML input: Hsp node {0} hseq length mismatch: from {1} to {2} length {3}".format( |
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136 nodeid(hsp), hfrom, hto, len(hseq))) |
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137 |
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138 |
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139 |
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140 @filter('len') |
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141 def blastxml_len(node): |
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142 if node.tag == 'Hsp': |
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143 return int(node['Hsp_align-len']) |
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144 elif node.tag == 'Iteration': |
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145 return int(node['Iteration_query-len']) |
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146 raise Exception("Unknown XML node type: "+node.tag) |
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147 |
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148 @filter |
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149 def nodeid(node): |
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150 id = [] |
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151 if node.tag == 'Hsp': |
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152 id.insert(0, node.Hsp_num.text) |
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153 node = node.getparent().getparent() |
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154 assert node.tag == 'Hit' |
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155 if node.tag == 'Hit': |
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156 id.insert(0, node.Hit_num.text) |
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157 node = node.getparent().getparent() |
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158 assert node.tag == 'Iteration' |
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159 if node.tag == 'Iteration': |
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160 id.insert(0, node['Iteration_iter-num'].text) |
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161 return '-'.join(id) |
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162 raise ValueError("The nodeid filter can only be applied to Hsp, Hit or Iteration nodes in a BlastXML document") |
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163 |
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164 |
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165 @filter |
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166 def asframe(frame): |
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167 if frame == 1: |
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168 return 'Plus' |
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169 elif frame == -1: |
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170 return 'Minus' |
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171 raise Exception("frame should be either +1 or -1") |
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172 |
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173 # def genelink(hit, type='genbank', hsp=None): |
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174 # if not isinstance(hit, six.string_types): |
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175 # hit = hitid(hit) |
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176 # link = "http://www.ncbi.nlm.nih.gov/nucleotide/{0}?report={1}&log$=nuclalign".format(hit, type) |
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177 # if hsp != None: |
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178 # link += "&from={0}&to={1}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to']) |
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179 # return link |
| 16 | 180 |
| 181 | |
| 182 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139 | |
| 183 # I've removed the html escapes, since html escaping is already being performed by the template engine. | |
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184 |
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185 # The r'\u0027' syntax doesn't work the way we need to in python 2.6 with unicode_literals |
| 16 | 186 _base_js_escapes = ( |
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187 ('\\', '\\u005C'), |
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188 ('\'', '\\u0027'), |
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189 ('"', '\\u0022'), |
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190 # ('>', '\\u003E'), |
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191 # ('<', '\\u003C'), |
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192 # ('&', '\\u0026'), |
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193 # ('=', '\\u003D'), |
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194 # ('-', '\\u002D'), |
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195 # (';', '\\u003B'), |
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196 (u'\u2028', '\\u2028'), |
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197 (u'\u2029', '\\u2029') |
| 16 | 198 ) |
| 199 | |
| 200 # Escape every ASCII character with a value less than 32. This is | |
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201 # needed a.o. to prevent html parsers from jumping out of javascript |
| 16 | 202 # parsing mode. |
| 203 _js_escapes = (_base_js_escapes + | |
| 204 tuple(('%c' % z, '\\u%04X' % z) for z in range(32))) | |
| 205 | |
| 206 @filter | |
| 207 def js_string_escape(value): | |
| 72 | 208 """ |
| 209 Javascript string literal escape. Note that this only escapes data | |
| 210 for embedding within javascript string literals, not in general | |
| 211 javascript snippets. | |
| 212 """ | |
| 16 | 213 |
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214 value = str(value) |
| 16 | 215 |
| 216 for bad, good in _js_escapes: | |
| 217 value = value.replace(bad, good) | |
| 218 | |
| 219 return value | |
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220 |
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221 @filter |
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222 def hits(result): |
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223 # Use findall so we get an empty list if there are no Hit elements at all |
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224 return result.Iteration_hits.findall('Hit') |
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225 |
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226 @filter('params') |
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227 def result_params(iteration): |
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228 return (('Query number', iteration['Iteration_iter-num']), |
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229 ('Query ID', iteration['Iteration_query-ID']), |
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230 ('Definition line', iteration['Iteration_query-def']), |
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231 ('Length', blastxml_len(iteration))) |
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232 |
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233 |
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234 class BlastVisualize: |
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235 |
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236 colors = ('black', 'blue', 'green', 'magenta', 'red') |
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237 |
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238 max_scale_labels = 10 |
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239 |
| 116 | 240 def __init__(self, input, templatedir, templatename, genelinks): |
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241 self.input = input |
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242 self.templatename = templatename |
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243 self.genelinks = genelinks |
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244 |
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245 self.blast = objectify.parse(self.input).getroot() |
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246 self.loader = jinja2.FileSystemLoader(searchpath=templatedir) |
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247 self.environment = jinja2.Environment(loader=self.loader, |
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248 lstrip_blocks=True, trim_blocks=True, autoescape=True) |
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249 |
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250 self._addfilters(self.environment) |
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251 |
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252 |
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253 def _addfilters(self, environment): |
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254 for filtername, funcname in _filters.items(): |
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255 try: |
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256 environment.filters[filtername] = getattr(self, funcname) |
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257 except AttributeError: |
| 75 | 258 try: |
| 259 environment.filters[filtername] = globals()[funcname] | |
| 260 except KeyError: | |
| 261 environment.filters[filtername] = getattr(builtins, funcname) | |
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262 |
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263 def render(self, output): |
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264 template = self.environment.get_template(self.templatename) |
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265 |
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266 params = (('Program', self.blast.BlastOutput_version), |
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267 ('Database', self.blast.BlastOutput_db), |
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268 ) |
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269 |
| 104 | 270 result = template.stream(blast=self.blast, |
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271 iterations=self.blast.BlastOutput_iterations.Iteration, |
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272 colors=self.colors, |
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273 params=params) |
| 104 | 274 |
| 275 result.dump(output) | |
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276 |
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277 @filter |
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278 def match_colors(self, result): |
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279 """ |
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280 An iterator that yields lists of length-color pairs. |
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281 """ |
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282 |
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283 query_length = blastxml_len(result) |
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284 |
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285 percent_multiplier = 100 / query_length |
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286 |
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287 for hit in hits(result): |
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288 # sort hotspots from short to long, so we can overwrite index colors of |
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289 # short matches with those of long ones. |
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290 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp)) |
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291 table = bytearray([255]) * query_length |
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292 for hsp in hotspots: |
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293 frm = hsp['Hsp_query-from'] - 1 |
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294 to = int(hsp['Hsp_query-to']) |
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295 table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm) |
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296 |
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297 matches = [] |
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298 last = table[0] |
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299 count = 0 |
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300 for i in range(query_length): |
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301 if table[i] == last: |
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302 count += 1 |
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303 continue |
| 16 | 304 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) |
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305 last = table[i] |
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306 count = 1 |
| 16 | 307 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) |
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308 |
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309 yield dict(colors=matches, hit=hit, defline=firsttitle(hit)) |
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310 |
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311 @filter |
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312 def queryscale(self, result): |
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313 query_length = blastxml_len(result) |
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314 skip = math.ceil(query_length / self.max_scale_labels) |
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315 percent_multiplier = 100 / query_length |
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316 for i in range(1, query_length+1): |
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317 if i % skip == 0: |
| 23 | 318 yield dict(label = i, width = skip * percent_multiplier) |
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319 if query_length % skip != 0: |
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320 yield dict(label = query_length, |
| 23 | 321 width = (query_length % skip) * percent_multiplier) |
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322 |
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323 @filter |
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324 def hit_info(self, result): |
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325 |
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326 query_length = blastxml_len(result) |
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327 |
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328 for hit in hits(result): |
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329 hsps = hit.Hit_hsps.Hsp |
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330 |
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331 # In python 2.6 array doesn't accept unicode type codes, but in 3.4 it requires them |
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332 typecode_B = builtin_str('B') |
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333 cover = array(typecode_B, [0]) * query_length |
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334 for hsp in hsps: |
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335 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = array(typecode_B, [1]) * blastxml_len(hsp) |
| 120 | 336 cover_count = cover.count(1) |
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337 |
| 120 | 338 best_hsp = max(hsps, key=lambda h: h['Hsp_bit-score']) |
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339 |
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340 yield dict(hit = hit, |
| 75 | 341 title = firsttitle(hit), |
| 120 | 342 maxscore = format(float(best_hsp['Hsp_bit-score']), '.1f'), |
| 343 e_value = format(float(best_hsp.Hsp_evalue), '.4'), | |
| 78 | 344 # float(...) because non-flooring division doesn't work with lxml elements in python 2.6 |
| 120 | 345 ident = format(float(best_hsp.Hsp_identity) / blastxml_len(best_hsp), '.0%'), |
| 346 totalscore = format(sum(hsp['Hsp_bit-score'] for hsp in hsps), '.1f'), | |
| 347 cover = format(cover_count / query_length, '.0%'), | |
| 348 ) | |
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349 |
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350 @filter |
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351 def genelink(self, hit, text=None, text_from='hitid', cssclass=None, display_nolink=True): |
| 96 | 352 """Create a html link from a hit node to a configured gene bank webpage. |
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353 text: The text of the link. If not set applies text_from. |
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354 text_from: string, if text is not specified, take it from specified source. Either 'hitid' (default) or 'dbname'. |
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355 cssclass: extra css classes that will be added to the <a> element |
| 96 | 356 display_nolink: boolean, if false don't display anything if no link can be created. Default True. |
| 357 """ | |
| 358 | |
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359 db = hit.getroottree().getroot().BlastOutput_db |
| 96 | 360 |
| 116 | 361 template = self.genelinks[db].template |
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362 |
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363 if text is None: |
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364 if text_from == 'hitid': |
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365 text = hitid(hit) |
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366 elif text_from == 'dbname': |
| 116 | 367 text = self.genelinks[db].dbname |
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368 else: |
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369 raise ValueError("Unknown value for text_from: '{0}'. Use 'hitid' or 'dbname'.".format(text_from)) |
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370 |
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371 if template is None: |
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372 return text if display_nolink else '' |
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373 |
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374 args = dict(id=hitid(hit).split('|'), |
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375 fullid=hitid(hit), |
| 104 | 376 defline=str(hit.Hit_def).split(' ', 1)[0].split('|'), |
| 377 fulldefline=str(hit.Hit_def).split(' ', 1)[0], | |
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378 accession=str(hit.Hit_accession)) |
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379 try: |
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380 link = template.format(**args) |
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381 except Exception as e: |
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382 warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e)) |
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383 return text if display_nolink else '' |
| 96 | 384 |
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385 classattr = 'class="{0}" '.format(jinja2.escape(cssclass)) if cssclass is not None else '' |
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386 return jinja2.Markup("<a {0}target=\"_top\" href=\"{1}\">{2}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text))) |
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387 |
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388 |
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389 genelinks_entry = namedtuple('genelinks_entry', 'dbname template') |
| 116 | 390 def read_blastdb(dir, default): |
| 391 links = defaultdict(lambda: default) | |
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392 # blastdb.loc, blastdb_p.loc, blastdb_d.loc, etc. |
| 101 | 393 files = sorted(glob.glob(path.join(dir, 'blastdb*.loc'))) |
| 394 # reversed, so blastdb.loc will take precedence | |
| 395 for f in reversed(files): | |
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396 try: |
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397 f = open(path.join(dir, f)) |
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398 for l in f.readlines(): |
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399 if l.strip().startswith('#'): |
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400 continue |
|
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401 line = l.rstrip('\n').split('\t') |
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402 try: |
| 116 | 403 links[line[2]] = genelinks_entry(dbname=line[3] or default.dbname, template=line[4]) |
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404 except IndexError: |
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405 continue |
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406 f.close() |
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407 except OSError: |
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408 continue |
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409 if not links: |
| 103 | 410 if not files: |
| 411 warnings.warn("No gene bank link templates found (no blastdb*.loc files found in {0})".format(dir)) | |
| 412 else: | |
| 413 warnings.warn("No gene bank link templates found in {0}".format(', '.join(files))) | |
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414 return links |
|
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415 |
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416 |
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417 def main(): |
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418 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja') |
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419 |
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420 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page", |
| 116 | 421 usage="{0} [-i] INPUT [-o OUTPUT] [--genelink-template URL_TEMPLATE] [--dbname DBNAME]".format(sys.argv[0])) |
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422 input_group = parser.add_mutually_exclusive_group(required=True) |
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423 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'), |
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424 help='The input Blast XML file, same as -i/--input') |
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425 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), |
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426 help='The input Blast XML file') |
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427 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout, |
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428 help='The output html file') |
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429 # We just want the file name here, so jinja can open the file |
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430 # itself. But it is easier to just use a FileType so argparse can |
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431 # handle the errors. This introduces a small race condition when |
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432 # jinja later tries to re-open the template file, but we don't |
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433 # care too much. |
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434 parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template, |
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435 help='The template file to use. Defaults to blast_html.html.jinja') |
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436 |
| 116 | 437 parser.add_argument('--dbname', type=str, default='Gene Bank', |
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438 help="The link text to use for external links to a gene bank database. Defaults to 'Gene Bank'") |
| 116 | 439 parser.add_argument('--genelink-template', metavar='URL_TEMPLATE', |
| 440 default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign', | |
| 441 help="""A link template to link hits to a gene bank webpage. The template string is a | |
| 442 Python format string. It can contain the following replacement elements: {id[N]}, {fullid}, | |
| 443 {defline[N]}, {fulldefline}, {accession}, where N is a number. id[N] and defline[N] will be | |
| 444 replaced by the Nth element of the id or defline, where '|' is the field separator. | |
| 445 | |
| 446 The default is 'http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign', | |
| 447 which is a link to the NCBI nucleotide database.""") | |
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448 |
| 116 | 449 parser.add_argument('--db-config-dir', |
| 450 help="""The directory where databases are configured in blastdb*.loc files. These files | |
| 451 are consulted for creating a gene bank link. The files should conform to the format that | |
| 452 Galaxy's BLAST expect, i.e. tab-separated tables (with lines starting with '#' ignored), | |
| 126 | 453 with two extra fields, for a total of five fields per line instead of three.. The third |
| 454 field of each line should be a database path as used by BLAST. The fourth field is the | |
| 455 human readable database name, and the fifth a template link to the gene bank conforming | |
| 456 to the syntax for the --genelink-template option. Entries in these config files override | |
| 457 links specified using --genelink-template and --dbname.""") | |
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458 |
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459 args = parser.parse_args() |
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460 if args.input == None: |
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461 args.input = args.positional_arg |
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462 if args.input == None: |
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463 parser.error('no input specified') |
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464 |
| 104 | 465 if six.PY2: |
| 466 # The argparse.FileType wrapper doesn't support an encoding | |
| 105 | 467 # argument, so for python 2 we need to wrap or reopen the |
| 468 # output. The input files are already read as utf-8 by the | |
| 104 | 469 # respective libraries. |
| 107 | 470 # |
| 104 | 471 # One option is using codecs, but the codecs' writelines() |
| 472 # method doesn't support streaming but collects all output and | |
| 105 | 473 # writes at once (see Python issues #5445 and #21910). On the |
| 474 # other hand the io module is slower (though not | |
| 475 # significantly). | |
| 104 | 476 |
| 477 # args.output = codecs.getwriter('utf-8')(args.output) | |
| 107 | 478 # def fixed_writelines(iter, self=args.output): |
| 479 # for i in iter: | |
| 480 # self.write(i) | |
| 481 # args.output.writelines = fixed_writelines | |
| 482 | |
| 483 args.output.close() | |
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484 args.output = io.open(args.output.name, 'w', encoding='utf-8') |
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485 |
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486 templatedir, templatename = path.split(args.template.name) |
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487 args.template.close() |
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488 if not templatedir: |
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489 templatedir = '.' |
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490 |
| 116 | 491 defaultentry = genelinks_entry(args.dbname, args.genelink_template) |
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492 if args.db_config_dir is None: |
| 116 | 493 genelinks = defaultdict(lambda: defaultentry) |
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494 elif not path.isdir(args.db_config_dir): |
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495 parser.error('db-config-dir does not exist or is not a directory') |
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496 else: |
| 116 | 497 genelinks = read_blastdb(args.db_config_dir, default=defaultentry) |
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498 |
| 116 | 499 b = BlastVisualize(args.input, templatedir, templatename, genelinks=genelinks) |
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500 b.render(args.output) |
| 104 | 501 args.output.close() |
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502 |
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503 |
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504 if __name__ == '__main__': |
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505 main() |
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506 |