| Previous changeset 117:8ae714069687 (2014-07-31) Next changeset 119:591dc9c24824 (2014-07-31) |
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Commit message:
fix for Rikilt issues 8, 11, 12, 14 |
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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 example3b.html test-data/blast xml example4.html test-data/blast xml example4b.html |
| b |
| diff -r 8ae714069687 -r 7f3f8c10f44b blast2html.html.jinja --- a/blast2html.html.jinja Thu Jul 31 14:55:07 2014 +0200 +++ b/blast2html.html.jinja Thu Jul 31 13:09:30 2014 +0200 |
| [ |
| @@ -422,9 +422,8 @@ {% for result in blast.BlastOutput_iterations.Iteration %} <div class=indexentry><a href="#match{{result|nodeid}}"> - {% set hits = result|hits %} {{result['Iteration_query-ID']}}: {{result['Iteration_query-def']}} - ({{result|len}} letters, {{hits|length}} hits) + ({{result|len}} letters, {{result|hits|length}} hits) </a></div> {% endfor %} @@ -476,7 +475,7 @@ <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div> <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div> <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div> - <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div> + <div class=graphicitem style="background-color: {{colors[4]}}">≥200</div> </div></div> <div style="clear: left"></div> @@ -611,12 +610,12 @@ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> </tr> <tr> - <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 }}({{ + <td>{{hsp['Hsp_bit-score']}} bits ({{hsp.Hsp_score}})</td> + <td>{{hsp.Hsp_evalue}}</td> + <td>{{ hsp.Hsp_identity }}/{{ hsp|len }} ({{ ((hsp.Hsp_identity|float)/hsp|len) | fmt('.0%') }})</td> <td>{{ hsp.Hsp_gaps }}/{{ hsp|len - }}({{ ((hsp.Hsp_gaps|float) / 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> |
| b |
| diff -r 8ae714069687 -r 7f3f8c10f44b blast2html.py --- a/blast2html.py Thu Jul 31 14:55:07 2014 +0200 +++ b/blast2html.py Thu Jul 31 13:09:30 2014 +0200 |
| b |
| @@ -342,7 +342,7 @@ maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))), totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))), cover = "{0:.0%}".format(cover_count / query_length), - e_value = "{0:.4g}".format(min(hsp_val('Hsp_evalue'))), + e_value = "{0:.4}".format(float(min(hsp_val('Hsp_evalue')))), # FIXME: is this the correct formula vv? # float(...) because non-flooring division doesn't work with lxml elements in python 2.6 ident = "{0:.0%}".format(float(min(float(hsp.Hsp_identity) / blastxml_len(hsp) for hsp in hsps)))) @@ -383,7 +383,7 @@ return text if display_nolink else '' classattr = 'class="{0}" '.format(jinja2.escape(cssclass)) if cssclass is not None else '' - return jinja2.Markup("<a {0}href=\"{1}\">{2}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text))) + return jinja2.Markup("<a {0}target=\"_top\" href=\"{1}\">{2}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text))) genelinks_entry = namedtuple('genelinks_entry', 'dbname template') |
| b |
| diff -r 8ae714069687 -r 7f3f8c10f44b test-data/blast xml example1.html --- a/test-data/blast xml example1.html Thu Jul 31 14:55:07 2014 +0200 +++ b/test-data/blast xml example1.html Thu Jul 31 13:09:30 2014 +0200 |
| b |
| b'@@ -440,7 +440,7 @@\n <div class=graphicitem style="background-color: blue">40\xe2\x80\x9350</div>\n <div class=graphicitem style="background-color: green">50\xe2\x80\x9380</div>\n <div class=graphicitem style="background-color: magenta">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: red">200\xe2\x89\xa4</div>\n+ <div class=graphicitem style="background-color: red">\xe2\x89\xa5200</div>\n </div></div>\n <div style="clear: left"></div>\n \n@@ -1868,7 +1868,7 @@\n <td>100%</td>\n <td>0.0007913</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5K_A?report=genbank&log$=nuclalign">3J5K_A</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5K_A?report=genbank&log$=nuclalign">3J5K_A</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-2"\n@@ -1881,7 +1881,7 @@\n <td>100%</td>\n <td>0.0007913</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5I_A?report=genbank&log$=nuclalign">3J5I_A</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5I_A?report=genbank&log$=nuclalign">3J5I_A</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-3"\n@@ -1894,7 +1894,7 @@\n <td>100%</td>\n <td>0.0007913</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5G_A?report=genbank&log$=nuclalign">3J5G_A</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5G_A?report=genbank&log$=nuclalign">3J5G_A</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-4"\n@@ -1907,7 +1907,7 @@\n <td>100%</td>\n <td>0.0007913</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5E_A?report=genbank&log$=nuclalign">3J5E_A</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5E_A?report=genbank&log$=nuclalign">3J5E_A</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-5"\n@@ -1920,7 +1920,7 @@\n <td>100%</td>\n <td>0.0007913</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5C_A?report=genbank&log$=nuclalign">3J5C_A</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5C_A?report=genbank&log$=nuclalign">3J5C_A</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-6"\n@@ -1933,7 +1933,7 @@\n <td>100%</td>\n <td>0.0007913</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5A_A?report=genbank&log$=nuclalign">3J5A_A</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J5A_A?report=genbank&log$=nuclalign">3J5A_A</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-7"\n@@ -1946,7 +1946,7 @@\n <td>100%</td>\n <td>0.0007913</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/3J58_A?report=genbank&log$=nuclalign">3J58_A</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J58_A?report=genbank&log$=nuclalign">3J58_A</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-8"\n@@ -1959,7 +1959,7 @@\n <t'..b' <td>0/8(0%)</td>\n+ <td>16.3517 bits (8)</td>\n+ <td>47.0266</td>\n+ <td>8/8 (100%)</td>\n+ <td>0/8 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -12454,13 +12454,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description1-99">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/4AQX_C?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/4AQX_C?report=genbank&log$=nuclalign">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>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</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/4AQX_C?report=genbank&log$=nuclalign">gi|393715375|pdb|4AQX|C</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/4AQX_C?report=genbank&log$=nuclalign">gi|393715375|pdb|4AQX|C</a>\n <span class=b>Length:</span> 14\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -12477,10 +12477,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>16.4 bits(8)</td>\n- <td>47.0</td>\n- <td>8/8(100%)</td>\n- <td>0/8(0%)</td>\n+ <td>16.3517 bits (8)</td>\n+ <td>47.0266</td>\n+ <td>8/8 (100%)</td>\n+ <td>0/8 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -12496,13 +12496,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description1-100">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/4AQU_C?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/4AQU_C?report=genbank&log$=nuclalign">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>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</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/4AQU_C?report=genbank&log$=nuclalign">gi|393715371|pdb|4AQU|C</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/4AQU_C?report=genbank&log$=nuclalign">gi|393715371|pdb|4AQU|C</a>\n <span class=b>Length:</span> 24\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -12519,10 +12519,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>16.4 bits(8)</td>\n- <td>47.0</td>\n- <td>8/8(100%)</td>\n- <td>0/8(0%)</td>\n+ <td>16.3517 bits (8)</td>\n+ <td>47.0266</td>\n+ <td>8/8 (100%)</td>\n+ <td>0/8 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n' |
| b |
| diff -r 8ae714069687 -r 7f3f8c10f44b test-data/blast xml example3.html --- a/test-data/blast xml example3.html Thu Jul 31 14:55:07 2014 +0200 +++ b/test-data/blast xml example3.html Thu Jul 31 13:09:30 2014 +0200 |
| b |
| b'@@ -719,7 +719,7 @@\n <div class=graphicitem style="background-color: blue">40\xe2\x80\x9350</div>\n <div class=graphicitem style="background-color: green">50\xe2\x80\x9380</div>\n <div class=graphicitem style="background-color: magenta">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: red">200\xe2\x89\xa4</div>\n+ <div class=graphicitem style="background-color: red">\xe2\x89\xa5200</div>\n </div></div>\n <div style="clear: left"></div>\n \n@@ -810,7 +810,7 @@\n <td>100%</td>\n <td>7.011e-08</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Subject_3</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Subject_3</a></td>\n </tr>\n </table>\n \n@@ -827,13 +827,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description3-1">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Subject_3</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Subject_3</a>\n <span class=b>Length:</span> 323\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -850,10 +850,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>37.4 bits(40)</td>\n- <td>0.0</td>\n- <td>20/20(100%)</td>\n- <td>0/20(0%)</td>\n+ <td>37.3537 bits (40)</td>\n+ <td>7.01052e-08</td>\n+ <td>20/20 (100%)</td>\n+ <td>0/20 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -952,7 +952,7 @@\n <div class=graphicitem style="background-color: blue">40\xe2\x80\x9350</div>\n <div class=graphicitem style="background-color: green">50\xe2\x80\x9380</div>\n <div class=graphicitem style="background-color: magenta">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: red">200\xe2\x89\xa4</div>\n+ <div class=graphicitem style="background-color: red">\xe2\x89\xa5200</div>\n </div></div>\n <div style="clear: left"></div>\n \n@@ -1043,7 +1043,7 @@\n <td>100%</td>\n <td>7.011e-08</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Subject_6</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Subject_6</a></td>\n </tr>\n </table>\n \n@@ -1060,13 +1060,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description6-1">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleoti'..b't_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Subject_7</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Subject_7</a>\n <span class=b>Length:</span> 4180\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -3253,10 +3253,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>89.7 bits(98)</td>\n- <td>0.0</td>\n- <td>64/74(86%)</td>\n- <td>0/74(0%)</td>\n+ <td>89.6514 bits (98)</td>\n+ <td>6.62923e-23</td>\n+ <td>64/74 (86%)</td>\n+ <td>0/74 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -3308,7 +3308,7 @@\n <div class=graphicitem style="background-color: blue">40\xe2\x80\x9350</div>\n <div class=graphicitem style="background-color: green">50\xe2\x80\x9380</div>\n <div class=graphicitem style="background-color: magenta">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: red">200\xe2\x89\xa4</div>\n+ <div class=graphicitem style="background-color: red">\xe2\x89\xa5200</div>\n </div></div>\n <div style="clear: left"></div>\n \n@@ -3400,7 +3400,7 @@\n <td>100%</td>\n <td>6.629e-23</td>\n <td>86%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a></td>\n </tr>\n </table>\n \n@@ -3417,13 +3417,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description56-1">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a>\n <span class=b>Length:</span> 4983\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -3440,10 +3440,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>89.7 bits(98)</td>\n- <td>0.0</td>\n- <td>64/74(86%)</td>\n- <td>0/74(0%)</td>\n+ <td>89.6514 bits (98)</td>\n+ <td>6.62923e-23</td>\n+ <td>64/74 (86%)</td>\n+ <td>0/74 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n' |
| b |
| diff -r 8ae714069687 -r 7f3f8c10f44b test-data/blast xml example3b.html --- a/test-data/blast xml example3b.html Thu Jul 31 14:55:07 2014 +0200 +++ b/test-data/blast xml example3b.html Thu Jul 31 13:09:30 2014 +0200 |
| b |
| b'@@ -719,7 +719,7 @@\n <div class=graphicitem style="background-color: blue">40\xe2\x80\x9350</div>\n <div class=graphicitem style="background-color: green">50\xe2\x80\x9380</div>\n <div class=graphicitem style="background-color: magenta">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: red">200\xe2\x89\xa4</div>\n+ <div class=graphicitem style="background-color: red">\xe2\x89\xa5200</div>\n </div></div>\n <div style="clear: left"></div>\n \n@@ -810,7 +810,7 @@\n <td>100%</td>\n <td>7.011e-08</td>\n <td>100%</td>\n- <td><a href="http://example.com/example-genebank?id=Subject_3">Subject_3</a></td>\n+ <td><a target="_top" href="http://example.com/example-genebank?id=Subject_3">Subject_3</a></td>\n </tr>\n </table>\n \n@@ -827,13 +827,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description3-1">Descriptions</a></div>\n- <a class="linkheader" href="http://example.com/example-genebank?id=Subject_3">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://example.com/example-genebank?id=Subject_3">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_3">Subject_3</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://example.com/example-genebank?id=Subject_3">Subject_3</a>\n <span class=b>Length:</span> 323\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -850,10 +850,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>37.4 bits(40)</td>\n- <td>0.0</td>\n- <td>20/20(100%)</td>\n- <td>0/20(0%)</td>\n+ <td>37.3537 bits (40)</td>\n+ <td>7.01052e-08</td>\n+ <td>20/20 (100%)</td>\n+ <td>0/20 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -952,7 +952,7 @@\n <div class=graphicitem style="background-color: blue">40\xe2\x80\x9350</div>\n <div class=graphicitem style="background-color: green">50\xe2\x80\x9380</div>\n <div class=graphicitem style="background-color: magenta">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: red">200\xe2\x89\xa4</div>\n+ <div class=graphicitem style="background-color: red">\xe2\x89\xa5200</div>\n </div></div>\n <div style="clear: left"></div>\n \n@@ -1043,7 +1043,7 @@\n <td>100%</td>\n <td>7.011e-08</td>\n <td>100%</td>\n- <td><a href="http://example.com/example-genebank?id=Subject_6">Subject_6</a></td>\n+ <td><a target="_top" href="http://example.com/example-genebank?id=Subject_6">Subject_6</a></td>\n </tr>\n </table>\n \n@@ -1060,13 +1060,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description6-1">Descriptions</a></div>\n- <a class="linkheader" href="http://example.com/example-genebank?id=Subject_6">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://example.com/example-genebank?id=Subject_6">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>AB209952.1|GenBank|in'..b'd=Subject_7">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://example.com/example-genebank?id=Subject_7">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_7">Subject_7</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://example.com/example-genebank?id=Subject_7">Subject_7</a>\n <span class=b>Length:</span> 4180\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -3253,10 +3253,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>89.7 bits(98)</td>\n- <td>0.0</td>\n- <td>64/74(86%)</td>\n- <td>0/74(0%)</td>\n+ <td>89.6514 bits (98)</td>\n+ <td>6.62923e-23</td>\n+ <td>64/74 (86%)</td>\n+ <td>0/74 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -3308,7 +3308,7 @@\n <div class=graphicitem style="background-color: blue">40\xe2\x80\x9350</div>\n <div class=graphicitem style="background-color: green">50\xe2\x80\x9380</div>\n <div class=graphicitem style="background-color: magenta">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: red">200\xe2\x89\xa4</div>\n+ <div class=graphicitem style="background-color: red">\xe2\x89\xa5200</div>\n </div></div>\n <div style="clear: left"></div>\n \n@@ -3400,7 +3400,7 @@\n <td>100%</td>\n <td>6.629e-23</td>\n <td>86%</td>\n- <td><a href="http://example.com/example-genebank?id=Subject_8">Subject_8</a></td>\n+ <td><a target="_top" href="http://example.com/example-genebank?id=Subject_8">Subject_8</a></td>\n </tr>\n </table>\n \n@@ -3417,13 +3417,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description56-1">Descriptions</a></div>\n- <a class="linkheader" href="http://example.com/example-genebank?id=Subject_8">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://example.com/example-genebank?id=Subject_8">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_8">Subject_8</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://example.com/example-genebank?id=Subject_8">Subject_8</a>\n <span class=b>Length:</span> 4983\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -3440,10 +3440,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>89.7 bits(98)</td>\n- <td>0.0</td>\n- <td>64/74(86%)</td>\n- <td>0/74(0%)</td>\n+ <td>89.6514 bits (98)</td>\n+ <td>6.62923e-23</td>\n+ <td>64/74 (86%)</td>\n+ <td>0/74 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n' |
| b |
| diff -r 8ae714069687 -r 7f3f8c10f44b test-data/blast xml example4.html --- a/test-data/blast xml example4.html Thu Jul 31 14:55:07 2014 +0200 +++ b/test-data/blast xml example4.html Thu Jul 31 13:09:30 2014 +0200 |
| b |
| b'@@ -473,7 +473,7 @@\n <div class=graphicitem style="background-color: blue">40\xe2\x80\x9350</div>\n <div class=graphicitem style="background-color: green">50\xe2\x80\x9380</div>\n <div class=graphicitem style="background-color: magenta">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: red">200\xe2\x89\xa4</div>\n+ <div class=graphicitem style="background-color: red">\xe2\x89\xa5200</div>\n </div></div>\n <div style="clear: left"></div>\n \n@@ -575,7 +575,7 @@\n <td>100%</td>\n <td>1.513e-07</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">5</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">5</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-2"\n@@ -588,7 +588,7 @@\n <td>100%</td>\n <td>1.513e-07</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">2</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">2</a></td>\n </tr>\n </table>\n \n@@ -605,13 +605,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description1-1">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">Gene Bank</a>\n </div>\n \n <div class=title>\n <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>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|5</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|5</a>\n <span class=b>Length:</span> 2457\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -628,10 +628,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>40.1 bits(20)</td>\n- <td>0.0</td>\n- <td>20/20(100%)</td>\n- <td>0/20(0%)</td>\n+ <td>40.14 bits (20)</td>\n+ <td>1.51296e-07</td>\n+ <td>20/20 (100%)</td>\n+ <td>0/20 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -647,13 +647,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description1-2">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a h'..b' <td><div><a href="#hit7-2"\n@@ -1480,7 +1480,7 @@\n <td>100%</td>\n <td>3.564e-15</td>\n <td>86%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">6</a></td>\n+ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">6</a></td>\n </tr>\n </table>\n \n@@ -1497,13 +1497,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description7-1">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|7</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|7</a>\n <span class=b>Length:</span> 4983\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -1520,10 +1520,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>67.9 bits(34)</td>\n- <td>0.0</td>\n- <td>64/74(86%)</td>\n- <td>0/74(0%)</td>\n+ <td>67.8929 bits (34)</td>\n+ <td>3.56369e-15</td>\n+ <td>64/74 (86%)</td>\n+ <td>0/74 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -1542,13 +1542,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description7-2">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|6</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|6</a>\n <span class=b>Length:</span> 4180\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -1565,10 +1565,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>67.9 bits(34)</td>\n- <td>0.0</td>\n- <td>64/74(86%)</td>\n- <td>0/74(0%)</td>\n+ <td>67.8929 bits (34)</td>\n+ <td>3.56369e-15</td>\n+ <td>64/74 (86%)</td>\n+ <td>0/74 (0%)</td>\n <td>Plus/Minus</td>\n </tr>\n </table>\n' |
| b |
| diff -r 8ae714069687 -r 7f3f8c10f44b test-data/blast xml example4b.html --- a/test-data/blast xml example4b.html Thu Jul 31 14:55:07 2014 +0200 +++ b/test-data/blast xml example4b.html Thu Jul 31 13:09:30 2014 +0200 |
| b |
| b'@@ -473,7 +473,7 @@\n <div class=graphicitem style="background-color: blue">40\xe2\x80\x9350</div>\n <div class=graphicitem style="background-color: green">50\xe2\x80\x9380</div>\n <div class=graphicitem style="background-color: magenta">80\xe2\x80\x93200</div>\n- <div class=graphicitem style="background-color: red">200\xe2\x89\xa4</div>\n+ <div class=graphicitem style="background-color: red">\xe2\x89\xa5200</div>\n </div></div>\n <div style="clear: left"></div>\n \n@@ -575,7 +575,7 @@\n <td>100%</td>\n <td>1.513e-07</td>\n <td>100%</td>\n- <td><a href="http://example.com/example-genebank/AB209952.1/">5</a></td>\n+ <td><a target="_top" href="http://example.com/example-genebank/AB209952.1/">5</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-2"\n@@ -588,7 +588,7 @@\n <td>100%</td>\n <td>1.513e-07</td>\n <td>100%</td>\n- <td><a href="http://example.com/example-genebank/DJ437711/">2</a></td>\n+ <td><a target="_top" href="http://example.com/example-genebank/DJ437711/">2</a></td>\n </tr>\n </table>\n \n@@ -605,13 +605,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description1-1">Descriptions</a></div>\n- <a class="linkheader" href="http://example.com/example-genebank/AB209952.1/">Example Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://example.com/example-genebank/AB209952.1/">Example Gene Bank</a>\n </div>\n \n <div class=title>\n <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>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/AB209952.1/">gnl|BL_ORD_ID|5</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://example.com/example-genebank/AB209952.1/">gnl|BL_ORD_ID|5</a>\n <span class=b>Length:</span> 2457\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -628,10 +628,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>40.1 bits(20)</td>\n- <td>0.0</td>\n- <td>20/20(100%)</td>\n- <td>0/20(0%)</td>\n+ <td>40.14 bits (20)</td>\n+ <td>1.51296e-07</td>\n+ <td>20/20 (100%)</td>\n+ <td>0/20 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -647,13 +647,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description1-2">Descriptions</a></div>\n- <a class="linkheader" href="http://example.com/example-genebank/DJ437711/">Example Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://example.com/example-genebank/DJ437711/">Example Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/DJ437711/">gnl|BL_ORD_ID|2</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://example.com/example-genebank/DJ437711/">gnl|BL_ORD_ID|2</a>\n <span cl'..b'd>\n <td>86%</td>\n- <td><a href="http://example.com/example-genebank/EUG/">7</a></td>\n+ <td><a target="_top" href="http://example.com/example-genebank/EUG/">7</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit7-2"\n@@ -1480,7 +1480,7 @@\n <td>100%</td>\n <td>3.564e-15</td>\n <td>86%</td>\n- <td><a href="http://example.com/example-genebank/AY326434/">6</a></td>\n+ <td><a target="_top" href="http://example.com/example-genebank/AY326434/">6</a></td>\n </tr>\n </table>\n \n@@ -1497,13 +1497,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description7-1">Descriptions</a></div>\n- <a class="linkheader" href="http://example.com/example-genebank/EUG/">Example Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://example.com/example-genebank/EUG/">Example Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/EUG/">gnl|BL_ORD_ID|7</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://example.com/example-genebank/EUG/">gnl|BL_ORD_ID|7</a>\n <span class=b>Length:</span> 4983\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -1520,10 +1520,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>67.9 bits(34)</td>\n- <td>0.0</td>\n- <td>64/74(86%)</td>\n- <td>0/74(0%)</td>\n+ <td>67.8929 bits (34)</td>\n+ <td>3.56369e-15</td>\n+ <td>64/74 (86%)</td>\n+ <td>0/74 (0%)</td>\n <td>Plus/Plus</td>\n </tr>\n </table>\n@@ -1542,13 +1542,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description7-2">Descriptions</a></div>\n- <a class="linkheader" href="http://example.com/example-genebank/AY326434/">Example Gene Bank</a>\n+ <a class="linkheader" target="_top" href="http://example.com/example-genebank/AY326434/">Example Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank/AY326434/">gnl|BL_ORD_ID|6</a>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://example.com/example-genebank/AY326434/">gnl|BL_ORD_ID|6</a>\n <span class=b>Length:</span> 4180\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -1565,10 +1565,10 @@\n <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n </tr>\n <tr>\n- <td>67.9 bits(34)</td>\n- <td>0.0</td>\n- <td>64/74(86%)</td>\n- <td>0/74(0%)</td>\n+ <td>67.8929 bits (34)</td>\n+ <td>3.56369e-15</td>\n+ <td>64/74 (86%)</td>\n+ <td>0/74 (0%)</td>\n <td>Plus/Minus</td>\n </tr>\n </table>\n' |