Mercurial > repos > jankanis > blast2html
changeset 119:591dc9c24824
tentative fix for Rikilt issue 10: don't sort hits ourselves but use blastxml ordering
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Thu, 31 Jul 2014 13:26:34 +0200 |
| parents | 7f3f8c10f44b |
| children | 2729c2326235 |
| files | blast2html.py test-data/blast xml example1.html |
| diffstat | 2 files changed, 182 insertions(+), 184 deletions(-) [+] |
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--- a/blast2html.py Thu Jul 31 13:09:30 2014 +0200 +++ b/blast2html.py Thu Jul 31 13:26:34 2014 +0200 @@ -219,10 +219,8 @@ @filter def hits(result): - # sort hits by longest hotspot first - return sorted(result.Iteration_hits.findall('Hit'), - key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp), - reverse=True) + # Use findall so we get an empty list if there are no Hit elements at all + return result.Iteration_hits.findall('Hit') @filter('params') def result_params(iteration):
--- a/test-data/blast xml example1.html Thu Jul 31 13:09:30 2014 +0200 +++ b/test-data/blast xml example1.html Thu Jul 31 13:26:34 2014 +0200 @@ -757,32 +757,6 @@ </a> <a class=matchresult - href="#hit1-30" - onmouseover='document.getElementById("defline1").innerHTML="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)"' - onmouseout='document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"' - title="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)"> - <div class="matchrow graphicrow"> - <div class="matchitem graphicitem" - style="background-color: black; width: 81.25%"></div> - <div class="matchitem graphicitem" - style="background-color: transparent; width: 18.75%"></div> - </div> - </a> - - <a class=matchresult - href="#hit1-35" - onmouseover='document.getElementById("defline1").innerHTML="Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)"' - onmouseout='document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"' - title="Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)"> - <div class="matchrow graphicrow"> - <div class="matchitem graphicitem" - style="background-color: black; width: 81.25%"></div> - <div class="matchitem graphicitem" - style="background-color: transparent; width: 18.75%"></div> - </div> - </a> - - <a class=matchresult href="#hit1-26" onmouseover='document.getElementById("defline1").innerHTML="Chain a, Model Of The Large Subunit Rna Based On A 5.5 A Cryo-em Map Of Triticum Aestivum Translating 80s Ribosome"' onmouseout='document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"' @@ -837,6 +811,19 @@ </a> <a class=matchresult + href="#hit1-30" + onmouseover='document.getElementById("defline1").innerHTML="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)"' + onmouseout='document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"' + title="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)"> + <div class="matchrow graphicrow"> + <div class="matchitem graphicitem" + style="background-color: black; width: 81.25%"></div> + <div class="matchitem graphicitem" + style="background-color: transparent; width: 18.75%"></div> + </div> + </a> + + <a class=matchresult href="#hit1-31" onmouseover='document.getElementById("defline1").innerHTML="Chain 0, The Re-refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution: More Complete Structure Of The L7/l12 And L1 Stalk, L5 And Lx Proteins"' onmouseout='document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"' @@ -887,6 +874,19 @@ </a> <a class=matchresult + href="#hit1-35" + onmouseover='document.getElementById("defline1").innerHTML="Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)"' + onmouseout='document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"' + title="Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)"> + <div class="matchrow graphicrow"> + <div class="matchitem graphicitem" + style="background-color: black; width: 81.25%"></div> + <div class="matchitem graphicitem" + style="background-color: transparent; width: 18.75%"></div> + </div> + </a> + + <a class=matchresult href="#hit1-36" onmouseover='document.getElementById("defline1").innerHTML="Chain 0, Crystal Structure Of Enhanced Macrolide Bound To 50s Ribosomal Subunit"' onmouseout='document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"' @@ -2183,32 +2183,6 @@ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/1C2W_B?report=genbank&log$=nuclalign">1C2W_B</a></td> </tr> <tr> - <td><div><a href="#hit1-30" - title="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)" - id="description1-30"> - Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit) - </a></div></td> - <td>18.3</td> - <td>36.7</td> - <td>81%</td> - <td>11.9</td> - <td>92%</td> - <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J44_1?report=genbank&log$=nuclalign">3J44_1</a></td> - </tr> - <tr> - <td><div><a href="#hit1-35" - title="Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)" - id="description1-35"> - Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna) - </a></div></td> - <td>18.3</td> - <td>36.7</td> - <td>81%</td> - <td>11.9</td> - <td>92%</td> - <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J2L_1?report=genbank&log$=nuclalign">3J2L_1</a></td> - </tr> - <tr> <td><div><a href="#hit1-26" title="Chain a, Model Of The Large Subunit Rna Based On A 5.5 A Cryo-em Map Of Triticum Aestivum Translating 80s Ribosome" id="description1-26"> @@ -2261,6 +2235,19 @@ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/4BYW_5?report=genbank&log$=nuclalign">4BYW_5</a></td> </tr> <tr> + <td><div><a href="#hit1-30" + title="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)" + id="description1-30"> + Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit) + </a></div></td> + <td>18.3</td> + <td>36.7</td> + <td>81%</td> + <td>11.9</td> + <td>92%</td> + <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J44_1?report=genbank&log$=nuclalign">3J44_1</a></td> + </tr> + <tr> <td><div><a href="#hit1-31" title="Chain 0, The Re-refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution: More Complete Structure Of The L7/l12 And L1 Stalk, L5 And Lx Proteins" id="description1-31"> @@ -2313,6 +2300,19 @@ <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3ZEX_B?report=genbank&log$=nuclalign">3ZEX_B</a></td> </tr> <tr> + <td><div><a href="#hit1-35" + title="Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)" + id="description1-35"> + Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna) + </a></div></td> + <td>18.3</td> + <td>36.7</td> + <td>81%</td> + <td>11.9</td> + <td>92%</td> + <td><a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J2L_1?report=genbank&log$=nuclalign">3J2L_1</a></td> + </tr> + <tr> <td><div><a href="#hit1-36" title="Chain 0, Crystal Structure Of Enhanced Macrolide Bound To 50s Ribosomal Subunit" id="description1-36"> @@ -6266,134 +6266,6 @@ </div> - <div class=alignment id=hit1-30> - - <div class=linkheader> - <div class=right><a href="#description1-30">Descriptions</a></div> - <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J44_1?report=genbank&log$=nuclalign">Gene Bank</a> - </div> - - <div class=title> - <p class=hittitle>Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)</p> - <p class=titleinfo> - <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J44_1?report=genbank&log$=nuclalign">gi|551701574|pdb|3J44|1</a> - <span class=b>Length:</span> 3049 - <span class=b>Number of Matches:</span> 2 - </p> - </div> - - - <div class=hotspot id=hotspot1-30-1> - <p class=range> - <span class=range>Range 1: 651 to 663</span> - </p> - - <table class=hotspotstable> - <tr> - <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> - </tr> - <tr> - <td>18.3341 bits (9)</td> - <td>11.9013</td> - <td>12/13 (92%)</td> - <td>0/13 (0%)</td> - <td>Plus/Plus</td> - </tr> - </table> - - <pre class=alignmentgraphic>Query 1 CGTCCGTCGTGAA 13 - |||||||| |||| -Subject 651 CGTCCGTCTTGAA 663</pre> - </div> - <div class=hotspot id=hotspot1-30-2> - <p class=range> - <span class=range>Range 2: 2705 to 2713</span> - </p> - - <table class=hotspotstable> - <tr> - <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> - </tr> - <tr> - <td>18.3341 bits (9)</td> - <td>11.9013</td> - <td>9/9 (100%)</td> - <td>0/9 (0%)</td> - <td>Plus/Plus</td> - </tr> - </table> - - <pre class=alignmentgraphic>Query 4 CCGTCGTGA 12 - ||||||||| -Subject 2705 CCGTCGTGA 2713</pre> - </div> - - </div> - - <div class=alignment id=hit1-35> - - <div class=linkheader> - <div class=right><a href="#description1-35">Descriptions</a></div> - <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J2L_1?report=genbank&log$=nuclalign">Gene Bank</a> - </div> - - <div class=title> - <p class=hittitle>Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)</p> - <p class=titleinfo> - <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J2L_1?report=genbank&log$=nuclalign">gi|428697991|pdb|3J2L|1</a> - <span class=b>Length:</span> 3049 - <span class=b>Number of Matches:</span> 2 - </p> - </div> - - - <div class=hotspot id=hotspot1-35-1> - <p class=range> - <span class=range>Range 1: 651 to 663</span> - </p> - - <table class=hotspotstable> - <tr> - <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> - </tr> - <tr> - <td>18.3341 bits (9)</td> - <td>11.9013</td> - <td>12/13 (92%)</td> - <td>0/13 (0%)</td> - <td>Plus/Plus</td> - </tr> - </table> - - <pre class=alignmentgraphic>Query 1 CGTCCGTCGTGAA 13 - |||||||| |||| -Subject 651 CGTCCGTCTTGAA 663</pre> - </div> - <div class=hotspot id=hotspot1-35-2> - <p class=range> - <span class=range>Range 2: 2705 to 2713</span> - </p> - - <table class=hotspotstable> - <tr> - <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> - </tr> - <tr> - <td>18.3341 bits (9)</td> - <td>11.9013</td> - <td>9/9 (100%)</td> - <td>0/9 (0%)</td> - <td>Plus/Plus</td> - </tr> - </table> - - <pre class=alignmentgraphic>Query 4 CCGTCGTGA 12 - ||||||||| -Subject 2705 CCGTCGTGA 2713</pre> - </div> - - </div> - <div class=alignment id=hit1-26> <div class=linkheader> @@ -6826,6 +6698,70 @@ </div> + <div class=alignment id=hit1-30> + + <div class=linkheader> + <div class=right><a href="#description1-30">Descriptions</a></div> + <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J44_1?report=genbank&log$=nuclalign">Gene Bank</a> + </div> + + <div class=title> + <p class=hittitle>Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)</p> + <p class=titleinfo> + <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J44_1?report=genbank&log$=nuclalign">gi|551701574|pdb|3J44|1</a> + <span class=b>Length:</span> 3049 + <span class=b>Number of Matches:</span> 2 + </p> + </div> + + + <div class=hotspot id=hotspot1-30-1> + <p class=range> + <span class=range>Range 1: 651 to 663</span> + </p> + + <table class=hotspotstable> + <tr> + <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> + </tr> + <tr> + <td>18.3341 bits (9)</td> + <td>11.9013</td> + <td>12/13 (92%)</td> + <td>0/13 (0%)</td> + <td>Plus/Plus</td> + </tr> + </table> + + <pre class=alignmentgraphic>Query 1 CGTCCGTCGTGAA 13 + |||||||| |||| +Subject 651 CGTCCGTCTTGAA 663</pre> + </div> + <div class=hotspot id=hotspot1-30-2> + <p class=range> + <span class=range>Range 2: 2705 to 2713</span> + </p> + + <table class=hotspotstable> + <tr> + <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> + </tr> + <tr> + <td>18.3341 bits (9)</td> + <td>11.9013</td> + <td>9/9 (100%)</td> + <td>0/9 (0%)</td> + <td>Plus/Plus</td> + </tr> + </table> + + <pre class=alignmentgraphic>Query 4 CCGTCGTGA 12 + ||||||||| +Subject 2705 CCGTCGTGA 2713</pre> + </div> + + </div> + <div class=alignment id=hit1-31> <div class=linkheader> @@ -7280,6 +7216,70 @@ </div> + <div class=alignment id=hit1-35> + + <div class=linkheader> + <div class=right><a href="#description1-35">Descriptions</a></div> + <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J2L_1?report=genbank&log$=nuclalign">Gene Bank</a> + </div> + + <div class=title> + <p class=hittitle>Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)</p> + <p class=titleinfo> + <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J2L_1?report=genbank&log$=nuclalign">gi|428697991|pdb|3J2L|1</a> + <span class=b>Length:</span> 3049 + <span class=b>Number of Matches:</span> 2 + </p> + </div> + + + <div class=hotspot id=hotspot1-35-1> + <p class=range> + <span class=range>Range 1: 651 to 663</span> + </p> + + <table class=hotspotstable> + <tr> + <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> + </tr> + <tr> + <td>18.3341 bits (9)</td> + <td>11.9013</td> + <td>12/13 (92%)</td> + <td>0/13 (0%)</td> + <td>Plus/Plus</td> + </tr> + </table> + + <pre class=alignmentgraphic>Query 1 CGTCCGTCGTGAA 13 + |||||||| |||| +Subject 651 CGTCCGTCTTGAA 663</pre> + </div> + <div class=hotspot id=hotspot1-35-2> + <p class=range> + <span class=range>Range 2: 2705 to 2713</span> + </p> + + <table class=hotspotstable> + <tr> + <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th> + </tr> + <tr> + <td>18.3341 bits (9)</td> + <td>11.9013</td> + <td>9/9 (100%)</td> + <td>0/9 (0%)</td> + <td>Plus/Plus</td> + </tr> + </table> + + <pre class=alignmentgraphic>Query 4 CCGTCGTGA 12 + ||||||||| +Subject 2705 CCGTCGTGA 2713</pre> + </div> + + </div> + <div class=alignment id=hit1-36> <div class=linkheader>