| Previous changeset 72:6ecbfebb9dd9 (2014-06-18) Next changeset 82:3338571b44cd (2014-06-23) |
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Commit message:
merge py2.6 branch |
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modified:
blast2html.html.jinja blast2html.py test-data/blast xml example1.html test-data/blast xml example3.html test-data/blast xml example4.html test-data/refresh_test_results.sh |
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| diff -r 6ecbfebb9dd9 -r 40ce2043006a blast2html.html.jinja --- a/blast2html.html.jinja Wed Jun 18 14:33:12 2014 +0200 +++ b/blast2html.html.jinja Thu Jun 19 17:00:29 2014 +0200 |
| [ |
| @@ -1,3 +1,4 @@ +{# -*- coding: utf-8 -*- #} <!DOCTYPE html> <html> <head> @@ -466,7 +467,7 @@ <div class=graphicrow> <div> {% for s in result|queryscale %} - <div class=graphicitem style="width: {{s.width}}%"> + <div class=graphicitem style="width: {{s.width|numfmt}}%"> {% if s.width > 3.0 %} <div>{{s.label}}</div> {% else %} @@ -489,7 +490,7 @@ <div class="matchrow graphicrow"> {% for hit in line.colors %} <div class="matchitem graphicitem" - style="background-color: {{hit[1]}}; width: {{hit[0]}}%"></div> + style="background-color: {{hit[1]}}; width: {{hit[0]|numfmt}}%"></div> {% endfor %} </div> </a> @@ -596,9 +597,9 @@ <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td> <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td> <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{ - (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td> + ((hsp.Hsp_identity|float)/hsp|len) | fmt('.0%') }})</td> <td>{{ hsp.Hsp_gaps }}/{{ hsp|len - }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td> + }}({{ ((hsp.Hsp_gaps|float) / hsp|len) | fmt('.0%') }})</td> <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td> </tr> </table> |
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| diff -r 6ecbfebb9dd9 -r 40ce2043006a blast2html.py --- a/blast2html.py Wed Jun 18 14:33:12 2014 +0200 +++ b/blast2html.py Thu Jun 19 17:00:29 2014 +0200 |
| [ |
| b'@@ -1,14 +1,18 @@\n #!/usr/bin/env python3\n # -*- coding: utf-8 -*-\n \n+# Actually this program works with both python 2 and 3, tested against python 2.6\n+\n # Copyright The Hyve B.V. 2014\n # License: GPL version 3 or (at your option) any higher version\n \n-from __future__ import unicode_literals\n+from __future__ import unicode_literals, division\n \n import sys\n import math\n import warnings\n+import six, codecs\n+from six.moves import builtins\n from os import path\n from itertools import repeat\n import argparse\n@@ -17,10 +21,10 @@\n \n \n \n-_filters = {}\n+_filters = dict(float=\'float\')\n def filter(func_or_name):\n "Decorator to register a function as filter in the current jinja environment"\n- if isinstance(func_or_name, str):\n+ if isinstance(func_or_name, six.string_types):\n def inner(func):\n _filters[func_or_name] = func.__name__\n return func\n@@ -46,6 +50,21 @@\n return format(float(val), fmt)\n \n @filter\n+def numfmt(val):\n+ """Format numbers in decimal notation, but without excessive trailing 0\'s.\n+ Default python float formatting will use scientific notation for some values,\n+ or append trailing zeros with the \'f\' format type, and the number of digits differs\n+ between python 2 and 3."""\n+ fpart, ipart = math.modf(val)\n+ if fpart == 0:\n+ return str(int(val))\n+ # round to 10 to get identical representations in python 2 and 3\n+ s = format(round(val, 10), \'.10f\').rstrip(\'0\')\n+ if s[-1] == \'.\':\n+ s += \'0\'\n+ return s\n+\n+@filter\n def firsttitle(hit):\n return hit.Hit_def.text.split(\'>\')[0]\n \n@@ -100,10 +119,10 @@\n hseq = hsp.Hsp_hseq.text\n \n if not qframe in (1, -1):\n- warnings.warn("Error in BlastXML input: Hsp node {} has a Hsp_query-frame of {}. (should be 1 or -1)".format(nodeid(hsp), qframe))\n+ 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))\n qframe = -1 if qframe < 0 else 1\n if not hframe in (1, -1):\n- warnings.warn("Error in BlastXML input: Hsp node {} has a Hsp_hit-frame of {}. (should be 1 or -1)".format(nodeid(hsp), hframe))\n+ 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))\n hframe = -1 if hframe < 0 else 1\n \n def split(txt):\n@@ -111,16 +130,16 @@\n \n for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), linewidth)):\n yield (\n- "Query {:>7} {} {}\\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) +\n- " {:7} {}\\n".format(\'\', mid) +\n- "Subject{:>7} {} {}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe)\n+ "Query {0:>7} {1} {2}\\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) +\n+ " {0:7} {1}\\n".format(\'\', mid) +\n+ "Subject{0:>7} {1} {2}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe)\n )\n \n if qfrom+(len(qseq)-1)*qframe != qto:\n- warnings.warn("Error in BlastXML input: Hsp node {} qseq length mismatch: from {} to {} length {}".format(\n+ warnings.warn("Error in BlastXML input: Hsp node {0} qseq length mismatch: from {1} to {2} length {3}".format(\n nodeid(hsp), qfrom, qto, len(qseq)))\n if hfrom+(len(hseq)-1)*hframe != hto:\n- warnings.warn("Error in BlastXML input: Hsp node {} hseq length mismatch: from {} to {} length {}".format(\n+ warnings.warn("Error in BlastXML input: Hsp node {0} hseq length mismatch: from {1} to {2} length {3}".format(\n nodeid(hsp), hfrom, hto, len(hseq)))\n \n \n@@ -159,29 +178,30 @@\n raise Exception("frame should be either +1 or -1")\n \n def genelink(hit, type=\'genbank\', hsp=None):\n- if not isinstance(hit, str):\n+ if not isinstance(hit, six.string_types):\n hit = hitid(hit)\n- link = "http://www.n'..b'E\'),\n+ # (\'<\', \'\\\\u003C\'),\n+ # (\'&\', \'\\\\u0026\'),\n+ # (\'=\', \'\\\\u003D\'),\n+ # (\'-\', \'\\\\u002D\'),\n+ # (\';\', \'\\\\u003B\'),\n+ (u\'\\u2028\', \'\\\\u2028\'),\n+ (u\'\\u2029\', \'\\\\u2029\')\n )\n \n # Escape every ASCII character with a value less than 32. This is\n@@ -198,7 +218,7 @@\n javascript snippets.\n """\n \n- value = str(value)\n+ value = six.text_type(value)\n \n for bad, good in _js_escapes:\n value = value.replace(bad, good)\n@@ -237,7 +257,10 @@\n try:\n environment.filters[filtername] = getattr(self, funcname)\n except AttributeError:\n- environment.filters[filtername] = globals()[funcname]\n+ try:\n+ environment.filters[filtername] = globals()[funcname]\n+ except KeyError:\n+ environment.filters[filtername] = getattr(builtins, funcname)\n \n def render(self, output):\n template = self.environment.get_template(self.templatename)\n@@ -249,13 +272,14 @@\n (\'Database\', self.blast.BlastOutput_db),\n )\n \n- output.write(template.render(blast=self.blast,\n- iterations=self.blast.BlastOutput_iterations.Iteration,\n- colors=self.colors,\n- # match_colors=self.match_colors(),\n- # hit_info=self.hit_info(),\n- genelink=genelink,\n- params=params))\n+ result = template.render(blast=self.blast,\n+ iterations=self.blast.BlastOutput_iterations.Iteration,\n+ colors=self.colors,\n+ genelink=genelink,\n+ params=params)\n+ if six.PY2:\n+ result = result.encode(\'utf-8\')\n+ output.write(result)\n \n @filter\n def match_colors(self, result):\n@@ -320,21 +344,22 @@\n return (float(hsp[path]) for hsp in hsps)\n \n yield dict(hit = hit,\n- title = firsttitle(hit),\n- maxscore = "{:.1f}".format(max(hsp_val(\'Hsp_bit-score\'))),\n- totalscore = "{:.1f}".format(sum(hsp_val(\'Hsp_bit-score\'))),\n- cover = "{:.0%}".format(cover_count / query_length),\n- e_value = "{:.4g}".format(min(hsp_val(\'Hsp_evalue\'))),\n+ title = firsttitle(hit),\n+ maxscore = "{0:.1f}".format(max(hsp_val(\'Hsp_bit-score\'))),\n+ totalscore = "{0:.1f}".format(sum(hsp_val(\'Hsp_bit-score\'))),\n+ cover = "{0:.0%}".format(cover_count / query_length),\n+ e_value = "{0:.4g}".format(min(hsp_val(\'Hsp_evalue\'))),\n # FIXME: is this the correct formula vv?\n- ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))),\n+ # float(...) because non-flooring division doesn\'t work with lxml elements in python 2.6\n+ ident = "{0:.0%}".format(float(min(float(hsp.Hsp_identity) / blastxml_len(hsp) for hsp in hsps))),\n accession = hit.Hit_accession)\n \n \n def main():\n default_template = path.join(path.dirname(__file__), \'blast2html.html.jinja\')\n- \n+\n parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",\n- usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))\n+ usage="{0} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))\n input_group = parser.add_mutually_exclusive_group(required=True)\n input_group.add_argument(\'positional_arg\', metavar=\'INPUT\', nargs=\'?\', type=argparse.FileType(mode=\'r\'),\n help=\'The input Blast XML file, same as -i/--input\')\n' |
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| diff -r 6ecbfebb9dd9 -r 40ce2043006a test-data/blast xml example1.html --- a/test-data/blast xml example1.html Wed Jun 18 14:33:12 2014 +0200 +++ b/test-data/blast xml example1.html Thu Jun 19 17:00:29 2014 +0200 |
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| b'@@ -468,7 +468,7 @@\n title="Chain A, E. Coli 70s-fmetval-trnaval Post-translocation Complex (post4, 50s Subunit)">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -479,7 +479,7 @@\n title="Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post3b, 50s Subunit)">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -490,7 +490,7 @@\n title="Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post3a, 50s Subunit)">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -501,7 +501,7 @@\n title="Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post2b, 50s Subunit)">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -512,7 +512,7 @@\n title="Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post2a, 50s Subunit)">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -523,7 +523,7 @@\n title="Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -534,7 +534,7 @@\n title="Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -545,7 +545,7 @@\n title="Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -556,7 +556,7 @@\n title="Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)">\n <div '..b' style="background-color: transparent; width: 25.0%"></div>\n- <div class="matchitem graphicitem"\n- style="background-color: black; width: 50.0%"></div>\n- <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 25.0%"></div>\n+ style="background-color: transparent; width: 25%"></div>\n+ <div class="matchitem graphicitem"\n+ style="background-color: black; width: 50%"></div>\n+ <div class="matchitem graphicitem"\n+ style="background-color: transparent; width: 25%"></div>\n </div>\n </a>\n \n@@ -1766,7 +1766,7 @@\n <div class="matchitem graphicitem"\n style="background-color: black; width: 56.25%"></div>\n <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 25.0%"></div>\n+ style="background-color: transparent; width: 25%"></div>\n </div>\n </a>\n \n@@ -1777,7 +1777,7 @@\n title="Chain A, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I. ">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 25.0%"></div>\n+ style="background-color: transparent; width: 25%"></div>\n <div class="matchitem graphicitem"\n style="background-color: black; width: 68.75%"></div>\n <div class="matchitem graphicitem"\n@@ -1792,11 +1792,11 @@\n title="Chain C, Crystal Structure Of I-Crei Complexed With Its Target Methylated At Position Plus 2 (In The B Strand) In The Presence Of Magnesium">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 25.0%"></div>\n- <div class="matchitem graphicitem"\n- style="background-color: black; width: 50.0%"></div>\n- <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 25.0%"></div>\n+ style="background-color: transparent; width: 25%"></div>\n+ <div class="matchitem graphicitem"\n+ style="background-color: black; width: 50%"></div>\n+ <div class="matchitem graphicitem"\n+ style="background-color: transparent; width: 25%"></div>\n </div>\n </a>\n \n@@ -1807,11 +1807,11 @@\n title="Chain C, Crystal Structure Of I-Crei Complexed With Its Target Methylated At Position Plus 2 (In The B Strand) In The Presence Of Calcium">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 25.0%"></div>\n- <div class="matchitem graphicitem"\n- style="background-color: black; width: 50.0%"></div>\n- <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 25.0%"></div>\n+ style="background-color: transparent; width: 25%"></div>\n+ <div class="matchitem graphicitem"\n+ style="background-color: black; width: 50%"></div>\n+ <div class="matchitem graphicitem"\n+ style="background-color: transparent; width: 25%"></div>\n </div>\n </a>\n \n' |
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| diff -r 6ecbfebb9dd9 -r 40ce2043006a test-data/blast xml example3.html --- a/test-data/blast xml example3.html Wed Jun 18 14:33:12 2014 +0200 +++ b/test-data/blast xml example3.html Thu Jun 19 17:00:29 2014 +0200 |
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| b'@@ -713,34 +713,34 @@\n <div>query:</div>\n <div class=graphicrow>\n <div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>2</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>4</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>6</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>8</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>10</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>12</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>14</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>16</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>18</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>20</div>\n </div>\n </div>\n@@ -755,7 +755,7 @@\n title="DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -952,34 +952,34 @@\n <div>query:</div>\n <div class=graphicrow>\n <div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>2</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>4</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>6</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>8</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>10</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>12</div>\n </div>\n- '..b'tem style="width: 10.8108108108%">\n <div>64</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>72</div>\n </div>\n- <div class=graphicitem style="width: 2.7027027027027026%">\n+ <div class=graphicitem style="width: 2.7027027027%">\n <div> </div>\n <div class=lastlabel>74</div>\n </div>\n@@ -3231,7 +3231,7 @@\n title="AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: green; width: 100.0%"></div>\n+ style="background-color: green; width: 100%"></div>\n </div>\n </a>\n \n@@ -3379,34 +3379,34 @@\n <div>query:</div>\n <div class=graphicrow>\n <div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>8</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>16</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>24</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>32</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>40</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>48</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>56</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>64</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>72</div>\n </div>\n- <div class=graphicitem style="width: 2.7027027027027026%">\n+ <div class=graphicitem style="width: 2.7027027027%">\n <div> </div>\n <div class=lastlabel>74</div>\n </div>\n@@ -3422,7 +3422,7 @@\n title="EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: green; width: 100.0%"></div>\n+ style="background-color: green; width: 100%"></div>\n </div>\n </a>\n \n' |
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| diff -r 6ecbfebb9dd9 -r 40ce2043006a test-data/blast xml example4.html --- a/test-data/blast xml example4.html Wed Jun 18 14:33:12 2014 +0200 +++ b/test-data/blast xml example4.html Thu Jun 19 17:00:29 2014 +0200 |
| b |
| b'@@ -465,34 +465,34 @@\n <div>query:</div>\n <div class=graphicrow>\n <div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>2</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>4</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>6</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>8</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>10</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>12</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>14</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>16</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>18</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>20</div>\n </div>\n </div>\n@@ -507,7 +507,7 @@\n title="AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -518,7 +518,7 @@\n title="DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 100.0%"></div>\n+ style="background-color: black; width: 100%"></div>\n </div>\n </a>\n \n@@ -747,34 +747,34 @@\n <div>query:</div>\n <div class=graphicrow>\n <div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>2</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>4</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ <div class=graphicitem style="width: 10%">\n <div>6</div>\n </div>\n- <div class=graphicitem style="width: 10.0%">\n+ '..b'struct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: black; width: 88.0%"></div>\n+ style="background-color: black; width: 88%"></div>\n <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 12.0%"></div>\n+ style="background-color: transparent; width: 12%"></div>\n </div>\n </a>\n \n@@ -1383,34 +1383,34 @@\n <div>query:</div>\n <div class=graphicrow>\n <div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>8</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>16</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>24</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>32</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>40</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>48</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>56</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>64</div>\n </div>\n- <div class=graphicitem style="width: 10.81081081081081%">\n+ <div class=graphicitem style="width: 10.8108108108%">\n <div>72</div>\n </div>\n- <div class=graphicitem style="width: 2.7027027027027026%">\n+ <div class=graphicitem style="width: 2.7027027027%">\n <div> </div>\n <div class=lastlabel>74</div>\n </div>\n@@ -1426,7 +1426,7 @@\n title="EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: green; width: 100.0%"></div>\n+ style="background-color: green; width: 100%"></div>\n </div>\n </a>\n \n@@ -1437,7 +1437,7 @@\n title="AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000">\n <div class="matchrow graphicrow">\n <div class="matchitem graphicitem"\n- style="background-color: green; width: 100.0%"></div>\n+ style="background-color: green; width: 100%"></div>\n </div>\n </a>\n \n' |
| b |
| diff -r 6ecbfebb9dd9 -r 40ce2043006a test-data/refresh_test_results.sh --- a/test-data/refresh_test_results.sh Wed Jun 18 14:33:12 2014 +0200 +++ b/test-data/refresh_test_results.sh Thu Jun 19 17:00:29 2014 +0200 |
| b |
| @@ -2,7 +2,9 @@ # run this from the directory it exists in to update the test outputs +set -eu + for i in 1 2 3 4 do - ../blast2html.py -i "blast xml example$i.xml" -o "blast xml example$i.html" + "$@" ../blast2html.py -i "blast xml example$i.xml" -o "blast xml example$i.html" done |