Mercurial > repos > jankanis > blast2html
changeset 108:b3b5ee557170 draft
update test
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Mon, 07 Jul 2014 11:42:43 +0200 |
| parents | a22c909c9b57 |
| children | ed71448ee154 |
| files | blast2html.py blast2html.xml test-data/blast xml example3.html test-data/blast xml example4.html test-data/refresh_test_results.sh |
| diffstat | 5 files changed, 73 insertions(+), 68 deletions(-) [+] |
line wrap: on
line diff
--- a/blast2html.py Mon Jul 07 11:29:10 2014 +0200 +++ b/blast2html.py Mon Jul 07 11:42:43 2014 +0200 @@ -409,7 +409,7 @@ default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja') parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page", - usage="{0} [-i] INPUT [-o OUTPUT]".format(sys.argv[0])) + usage="{0} [-i] INPUT [-o OUTPUT] [--genelink-template URL_TEMPLATE]".format(sys.argv[0])) input_group = parser.add_mutually_exclusive_group(required=True) input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'), help='The input Blast XML file, same as -i/--input') @@ -426,7 +426,8 @@ help='The template file to use. Defaults to blast_html.html.jinja') dblink_group = parser.add_mutually_exclusive_group() - dblink_group.add_argument('--genelink-template', default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign', + dblink_group.add_argument('--genelink-template', metavar='URL_TEMPLATE', + default='http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&log$=nuclalign', help="""A link template to link hits to a gene bank webpage. The template string is a Python format string. It can contain the following replacement elements: {id[N]}, {fullid}, {defline[N]}, {fulldefline}, {accession}, where N is a number. id[N] and defline[N] will be @@ -451,14 +452,15 @@ if six.PY2: # The argparse.FileType wrapper doesn't support an encoding - # argument or such, so for python 2 we need to wrap or reopen - # the output. The input files are already read as utf-8 by the + # argument, so for python 2 we need to wrap or reopen the + # output. The input files are already read as utf-8 by the # respective libraries. # One option is using codecs, but the codecs' writelines() # method doesn't support streaming but collects all output and - # writes at once. On the other hand the io module is slower - # (though not significantly). + # writes at once (see Python issues #5445 and #21910). On the + # other hand the io module is slower (though not + # significantly). # args.output = codecs.getwriter('utf-8')(args.output) args.output = io.open(args.output.name, 'w')
--- a/blast2html.xml Mon Jul 07 11:29:10 2014 +0200 +++ b/blast2html.xml Mon Jul 07 11:42:43 2014 +0200 @@ -25,19 +25,19 @@ <tests> <test> <param name="input" value="blast xml example1.xml"/> - <output name="out_file1" file="blast xml example1.html"/> + <output name="output" file="blast xml example1.html"/> </test> <test> <param name="input" value="blast xml example2.xml"/> - <output name="out_file1" file="blast xml example2.html"/> + <output name="output" file="blast xml example2.html"/> </test> <test> <param name="input" value="blast xml example3.xml"/> - <output name="out_file1" file="blast xml example3.html"/> + <output name="output" file="blast xml example3.html"/> </test> <test> <param name="input" value="blast xml example4.xml"/> - <output name="out_file1" file="blast xml example4.html"/> + <output name="output" file="blast xml example4.html"/> </test> </tests>
--- a/test-data/blast xml example3.html Mon Jul 07 11:29:10 2014 +0200 +++ b/test-data/blast xml example3.html Mon Jul 07 11:42:43 2014 +0200 @@ -794,7 +794,7 @@ <td>100%</td> <td>7.011e-08</td> <td>100%</td> - <td><a href="http://example.com/example-genebank?id=Subject_3">Subject_3</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Subject_3</a></td> </tr> </table> @@ -811,13 +811,13 @@ <div class=linkheader> <div class=right><a href="#description3-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank?id=Subject_3">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_3">Subject_3</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Subject_3</a> <span class=b>Length:</span> 323 <span class=b>Number of Matches:</span> 1 </p> @@ -1030,7 +1030,7 @@ <td>100%</td> <td>7.011e-08</td> <td>100%</td> - <td><a href="http://example.com/example-genebank?id=Subject_6">Subject_6</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Subject_6</a></td> </tr> </table> @@ -1047,13 +1047,13 @@ <div class=linkheader> <div class=right><a href="#description6-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank?id=Subject_6">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_6">Subject_6</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Subject_6</a> <span class=b>Length:</span> 2457 <span class=b>Number of Matches:</span> 1 </p> @@ -1502,7 +1502,7 @@ <td>85%</td> <td>2.981e-06</td> <td>100%</td> - <td><a href="http://example.com/example-genebank?id=Subject_2">Subject_2</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_2?report=genbank&log$=nuclalign">Subject_2</a></td> </tr> </table> @@ -1519,13 +1519,13 @@ <div class=linkheader> <div class=right><a href="#description18-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank?id=Subject_2">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_2?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>AJ308515.1|GenBank|insert_GTS-40-3-2|Synthetic_construct_for_NOS_3'UTR/plant_junction_region.|-9105899556052450000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_2">Subject_2</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_2?report=genbank&log$=nuclalign">Subject_2</a> <span class=b>Length:</span> 1045 <span class=b>Number of Matches:</span> 1 </p> @@ -1686,7 +1686,7 @@ <td>100%</td> <td>7.011e-08</td> <td>100%</td> - <td><a href="http://example.com/example-genebank?id=Subject_3">Subject_3</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Subject_3</a></td> </tr> </table> @@ -1703,13 +1703,13 @@ <div class=linkheader> <div class=right><a href="#description19-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank?id=Subject_3">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_3">Subject_3</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Subject_3</a> <span class=b>Length:</span> 323 <span class=b>Number of Matches:</span> 1 </p> @@ -1922,7 +1922,7 @@ <td>100%</td> <td>7.011e-08</td> <td>100%</td> - <td><a href="http://example.com/example-genebank?id=Subject_6">Subject_6</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Subject_6</a></td> </tr> </table> @@ -1939,13 +1939,13 @@ <div class=linkheader> <div class=right><a href="#description22-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank?id=Subject_6">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>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</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_6">Subject_6</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Subject_6</a> <span class=b>Length:</span> 2457 <span class=b>Number of Matches:</span> 1 </p> @@ -2727,7 +2727,7 @@ <td>100%</td> <td>9.338e-08</td> <td>92%</td> - <td><a href="http://example.com/example-genebank?id=Subject_7">Subject_7</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Subject_7</a></td> </tr> </table> @@ -2744,13 +2744,13 @@ <div class=linkheader> <div class=right><a href="#description47-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank?id=Subject_7">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_7">Subject_7</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Subject_7</a> <span class=b>Length:</span> 4180 <span class=b>Number of Matches:</span> 1 </p> @@ -2908,7 +2908,7 @@ <td>100%</td> <td>9.338e-08</td> <td>92%</td> - <td><a href="http://example.com/example-genebank?id=Subject_8">Subject_8</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a></td> </tr> </table> @@ -2925,13 +2925,13 @@ <div class=linkheader> <div class=right><a href="#description48-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank?id=Subject_8">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_8">Subject_8</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a> <span class=b>Length:</span> 4983 <span class=b>Number of Matches:</span> 1 </p> @@ -3249,7 +3249,7 @@ <td>100%</td> <td>6.629e-23</td> <td>86%</td> - <td><a href="http://example.com/example-genebank?id=Subject_7">Subject_7</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Subject_7</a></td> </tr> </table> @@ -3266,13 +3266,13 @@ <div class=linkheader> <div class=right><a href="#description55-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank?id=Subject_7">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_7">Subject_7</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Subject_7</a> <span class=b>Length:</span> 4180 <span class=b>Number of Matches:</span> 1 </p> @@ -3437,7 +3437,7 @@ <td>100%</td> <td>6.629e-23</td> <td>86%</td> - <td><a href="http://example.com/example-genebank?id=Subject_8">Subject_8</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a></td> </tr> </table> @@ -3454,13 +3454,13 @@ <div class=linkheader> <div class=right><a href="#description56-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank?id=Subject_8">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_8">Subject_8</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a> <span class=b>Length:</span> 4983 <span class=b>Number of Matches:</span> 1 </p>
--- a/test-data/blast xml example4.html Mon Jul 07 11:29:10 2014 +0200 +++ b/test-data/blast xml example4.html Mon Jul 07 11:42:43 2014 +0200 @@ -557,7 +557,7 @@ <td>100%</td> <td>1.513e-07</td> <td>100%</td> - <td><a href="http://example.com/example-genebank/AB209952.1/">5</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">5</a></td> </tr> <tr> <td><div><a href="#hit1-2" @@ -570,7 +570,7 @@ <td>100%</td> <td>1.513e-07</td> <td>100%</td> - <td><a href="http://example.com/example-genebank/DJ437711/">2</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">2</a></td> </tr> </table> @@ -587,13 +587,13 @@ <div class=linkheader> <div class=right><a href="#description1-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AB209952.1/">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>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</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/AB209952.1/">gnl|BL_ORD_ID|5</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|5</a> <span class=b>Length:</span> 2457 <span class=b>Number of Matches:</span> 1 </p> @@ -629,13 +629,13 @@ <div class=linkheader> <div class=right><a href="#description1-2">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/DJ437711/">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/DJ437711/">gnl|BL_ORD_ID|2</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|2</a> <span class=b>Length:</span> 323 <span class=b>Number of Matches:</span> 1 </p> @@ -846,7 +846,7 @@ <td>100%</td> <td>1.513e-07</td> <td>100%</td> - <td><a href="http://example.com/example-genebank/AB209952.1/">5</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">5</a></td> </tr> <tr> <td><div><a href="#hit3-2" @@ -859,7 +859,7 @@ <td>100%</td> <td>1.513e-07</td> <td>100%</td> - <td><a href="http://example.com/example-genebank/DJ437711/">2</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">2</a></td> </tr> <tr> <td><div><a href="#hit3-3" @@ -872,7 +872,7 @@ <td>85%</td> <td>9.334e-06</td> <td>100%</td> - <td><a href="http://example.com/example-genebank/AJ308515.1/">1</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/1?report=genbank&log$=nuclalign">1</a></td> </tr> </table> @@ -889,13 +889,13 @@ <div class=linkheader> <div class=right><a href="#description3-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AB209952.1/">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/AB209952.1/">gnl|BL_ORD_ID|5</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|5</a> <span class=b>Length:</span> 2457 <span class=b>Number of Matches:</span> 1 </p> @@ -931,13 +931,13 @@ <div class=linkheader> <div class=right><a href="#description3-2">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/DJ437711/">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/DJ437711/">gnl|BL_ORD_ID|2</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|2</a> <span class=b>Length:</span> 323 <span class=b>Number of Matches:</span> 1 </p> @@ -973,13 +973,13 @@ <div class=linkheader> <div class=right><a href="#description3-3">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AJ308515.1/">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/1?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>AJ308515.1|GenBank|insert_GTS-40-3-2|Synthetic_construct_for_NOS_3'UTR/plant_junction_region.|-9105899556052450000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/AJ308515.1/">gnl|BL_ORD_ID|1</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/1?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|1</a> <span class=b>Length:</span> 1045 <span class=b>Number of Matches:</span> 1 </p> @@ -1204,7 +1204,7 @@ <td>88%</td> <td>3.148e-06</td> <td>95%</td> - <td><a href="http://example.com/example-genebank/EUG/">7</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">7</a></td> </tr> <tr> <td><div><a href="#hit6-2" @@ -1217,7 +1217,7 @@ <td>88%</td> <td>3.148e-06</td> <td>95%</td> - <td><a href="http://example.com/example-genebank/AY326434/">6</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">6</a></td> </tr> </table> @@ -1234,13 +1234,13 @@ <div class=linkheader> <div class=right><a href="#description6-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/EUG/">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/EUG/">gnl|BL_ORD_ID|7</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|7</a> <span class=b>Length:</span> 4983 <span class=b>Number of Matches:</span> 1 </p> @@ -1276,13 +1276,13 @@ <div class=linkheader> <div class=right><a href="#description6-2">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AY326434/">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/AY326434/">gnl|BL_ORD_ID|6</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|6</a> <span class=b>Length:</span> 4180 <span class=b>Number of Matches:</span> 1 </p> @@ -1455,7 +1455,7 @@ <td>100%</td> <td>3.564e-15</td> <td>86%</td> - <td><a href="http://example.com/example-genebank/EUG/">7</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">7</a></td> </tr> <tr> <td><div><a href="#hit7-2" @@ -1468,7 +1468,7 @@ <td>100%</td> <td>3.564e-15</td> <td>86%</td> - <td><a href="http://example.com/example-genebank/AY326434/">6</a></td> + <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">6</a></td> </tr> </table> @@ -1485,13 +1485,13 @@ <div class=linkheader> <div class=right><a href="#description7-1">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/EUG/">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/EUG/">gnl|BL_ORD_ID|7</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|7</a> <span class=b>Length:</span> 4983 <span class=b>Number of Matches:</span> 1 </p> @@ -1530,13 +1530,13 @@ <div class=linkheader> <div class=right><a href="#description7-2">Descriptions</a></div> - <a class="linkheader" href="http://example.com/example-genebank/AY326434/">Gene Bank</a> + <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">Gene Bank</a> </div> <div class=title> <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p> <p class=titleinfo> - <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/AY326434/">gnl|BL_ORD_ID|6</a> + <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|6</a> <span class=b>Length:</span> 4180 <span class=b>Number of Matches:</span> 1 </p>
--- a/test-data/refresh_test_results.sh Mon Jul 07 11:29:10 2014 +0200 +++ b/test-data/refresh_test_results.sh Mon Jul 07 11:42:43 2014 +0200 @@ -4,8 +4,11 @@ set -eu -"$@" ../blast2html.py -i "blast xml example1.xml" -o "blast xml example1.html" -"$@" ../blast2html.py -i "blast xml example2.xml" -o "blast xml example2.html" -"$@" ../blast2html.py -i "blast xml example3.xml" -o "blast xml example3.html" --genelink-template 'http://example.com/example-genebank?id={fullid}' -"$@" ../blast2html.py -i "blast xml example4.xml" -o "blast xml example4.html" --db-config-dir . +for i in 1 2 3 4 +do + "$@" ../blast2html.py -i "blast xml example$i.xml" -o "blast xml example$i.html" +done +"$@" ../blast2html.py -i "blast xml example3.xml" -o "blast xml example3b.html" --genelink-template 'http://example.com/example-genebank?id={fullid}' +"$@" ../blast2html.py -i "blast xml example4.xml" -o "blast xml example4b.html" --db-config-dir . +