Mercurial > repos > jankanis > blast2html

annotate visualise.py @ 5:1df2bfce5c24

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first features are working, partial match table
author Jan Kanis <jan.code@jankanis.nl>
date Wed, 07 May 2014 18:49:54 +0200
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children 9e7927673089
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1 #!/usr/bin/env python3
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2
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3 # Copyright The Hyve B.V. 2014
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4 # License: GPL version 3 or higher
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5
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6 import sys
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7 import warnings
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8 from itertools import repeat
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9 from lxml import objectify
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10 import jinja2
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11
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12
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13 def color_idx(length):
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14 if length < 40:
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15 return 0
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16 elif length < 50:
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17 return 1
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18 elif length < 80:
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19 return 2
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20 elif length < 200:
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21 return 3
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22 return 4
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24
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25 colors = ['black', 'blue', 'green', 'magenta', 'red']
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26
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27 blast = objectify.parse('blast xml example1.xml').getroot()
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28 loader = jinja2.FileSystemLoader(searchpath='.')
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29 environment = jinja2.Environment(loader=loader)
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30 environment.filters['color'] = lambda length: match_colors[color_idx(length)]
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31
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32 def match_colors():
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33 """
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34 An iterator that yields lists of length-color pairs.
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35 """
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36
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37 hits = blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit
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38 query_length = blast["BlastOutput_query-len"]
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39 # sort hits by longest hotspot first
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40 hits = sorted(hits, key=lambda h: max(hsp['Hsp_align-len'] for hsp in h.Hit_hsps.Hsp), reverse=True)
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41
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42 for hit in hits:
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43 # sort hotspots from short to long, so we can overwrite index colors of
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44 # short matches with those of long ones.
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45 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: hsp['Hsp_align-len'])
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46 table = bytearray([255]) * query_length
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47 for hsp in hotspots:
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48 frm = hsp['Hsp_query-from'] - 1
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49 to = hsp['Hsp_query-to'] - 1
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50 table[frm:to] = repeat(color_idx(hsp['Hsp_align-len']), to - frm)
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51
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52 matches = []
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53 last = table[0]
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54 count = 0
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55 for i in range(int(query_length)):
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56 if table[i] == last:
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57 count += 1
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58 continue
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59 matches.append((count, colors[last] if last != 255 else 'none'))
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60 last = table[i]
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61 count = 1
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62 matches.append((count, colors[last] if last != 255 else 'none'))
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63
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64 yield dict(colors=matches, link="#hit"+hit.Hit_num.text)
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65
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66
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67 def main():
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68 template = environment.get_template('visualise.html.jinja')
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69
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70 params = (('Query ID', blast["BlastOutput_query-ID"]),
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71 ('Query definition', blast["BlastOutput_query-def"]),
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72 ('Query length', blast["BlastOutput_query-len"]),
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73 ('Program', blast.BlastOutput_version),
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74 ('Database', blast.BlastOutput_db),
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75 )
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76
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77 if len(blast.BlastOutput_iterations.Iteration) > 1:
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78 warnings.warn("Multiple 'Iteration' elements found, showing only the first")
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79
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80 sys.stdout.write(template.render(blast=blast,
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81 hits=blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit,
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82 colors=colors,
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83 match_colors=match_colors(),
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84 params=params))
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85
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86 main()