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Changeset 119:591dc9c24824 (2014-07-31)

Previous changeset 118:7f3f8c10f44b (2014-07-31) Next changeset 120:2729c2326235 (2014-07-31)

Commit message:
tentative fix for Rikilt issue 10: don't sort hits ourselves but use blastxml ordering

modified:
blast2html.py
test-data/blast xml example1.html

diff -r 7f3f8c10f44b -r 591dc9c24824 blast2html.py
--- 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):

diff -r 7f3f8c10f44b -r 591dc9c24824 test-data/blast xml example1.html
--- 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

b'@@ -757,32 +757,6 @@\n </a>\n \n <a class=matchresult\n- href="#hit1-30"\n- onmouseover=\'document.getElementById("defline1").innerHTML="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)"\'\n- onmouseout=\'document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"\'\n- title="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)">\n- <div class="matchrow graphicrow">\n- <div class="matchitem graphicitem"\n- style="background-color: black; width: 81.25%"></div>\n- <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 18.75%"></div>\n- </div>\n- </a>\n-\n- <a class=matchresult\n- href="#hit1-35"\n- 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)"\'\n- onmouseout=\'document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"\'\n- title="Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)">\n- <div class="matchrow graphicrow">\n- <div class="matchitem graphicitem"\n- style="background-color: black; width: 81.25%"></div>\n- <div class="matchitem graphicitem"\n- style="background-color: transparent; width: 18.75%"></div>\n- </div>\n- </a>\n-\n- <a class=matchresult\n href="#hit1-26"\n 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"\'\n onmouseout=\'document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"\'\n@@ -837,6 +811,19 @@\n </a>\n \n <a class=matchresult\n+ href="#hit1-30"\n+ onmouseover=\'document.getElementById("defline1").innerHTML="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)"\'\n+ onmouseout=\'document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"\'\n+ title="Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)">\n+ <div class="matchrow graphicrow">\n+ <div class="matchitem graphicitem"\n+ style="background-color: black; width: 81.25%"></div>\n+ <div class="matchitem graphicitem"\n+ style="background-color: transparent; width: 18.75%"></div>\n+ </div>\n+ </a>\n+\n+ <a class=matchresult\n href="#hit1-31"\n 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"\'\n onmouseout=\'document.getElementById("defline1").innerHTML="Mouse-over to show defline and scores, click to show alignments"\'\n@@ -887,6 +874,19 @@\n </a>\n \n <a class=matchresult\n+ href="#hi'..b' <pre class=alignmentgraphic>Query 1 CGTCCGTCGTGAA 13\n+ |||||||| ||||\n+Subject 651 CGTCCGTCTTGAA 663</pre>\n+ </div>\n+ <div class=hotspot id=hotspot1-30-2>\n+ <p class=range>\n+ <span class=range>Range 2: 2705 to 2713</span>\n+ </p>\n+\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>18.3341 bits (9)</td>\n+ <td>11.9013</td>\n+ <td>9/9 (100%)</td>\n+ <td>0/9 (0%)</td>\n+ <td>Plus/Plus</td>\n+ </tr>\n+ </table>\n+\n+ <pre class=alignmentgraphic>Query 4 CCGTCGTGA 12\n+ |||||||||\n+Subject 2705 CCGTCGTGA 2713</pre>\n+ </div>\n+\n+ </div>\n+\n <div class=alignment id=hit1-31>\n \n <div class=linkheader>\n@@ -7280,6 +7216,70 @@\n \n </div>\n \n+ <div class=alignment id=hit1-35>\n+\n+ <div class=linkheader>\n+ <div class=right><a href="#description1-35">Descriptions</a></div>\n+ <a class="linkheader" target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J2L_1?report=genbank&log$=nuclalign">Gene Bank</a>\n+ </div>\n+\n+ <div class=title>\n+ <p class=hittitle>Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)</p>\n+ <p class=titleinfo>\n+ <span class=b>Sequence ID:</span> <a target="_top" href="http://www.ncbi.nlm.nih.gov/nucleotide/3J2L_1?report=genbank&log$=nuclalign">gi|428697991|pdb|3J2L|1</a>\n+ <span class=b>Length:</span> 3049\n+ <span class=b>Number of Matches:</span> 2\n+ </p>\n+ </div>\n+\n+\n+ <div class=hotspot id=hotspot1-35-1>\n+ <p class=range>\n+ <span class=range>Range 1: 651 to 663</span>\n+ </p>\n+\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>18.3341 bits (9)</td>\n+ <td>11.9013</td>\n+ <td>12/13 (92%)</td>\n+ <td>0/13 (0%)</td>\n+ <td>Plus/Plus</td>\n+ </tr>\n+ </table>\n+\n+ <pre class=alignmentgraphic>Query 1 CGTCCGTCGTGAA 13\n+ |||||||| ||||\n+Subject 651 CGTCCGTCTTGAA 663</pre>\n+ </div>\n+ <div class=hotspot id=hotspot1-35-2>\n+ <p class=range>\n+ <span class=range>Range 2: 2705 to 2713</span>\n+ </p>\n+\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>18.3341 bits (9)</td>\n+ <td>11.9013</td>\n+ <td>9/9 (100%)</td>\n+ <td>0/9 (0%)</td>\n+ <td>Plus/Plus</td>\n+ </tr>\n+ </table>\n+\n+ <pre class=alignmentgraphic>Query 4 CCGTCGTGA 12\n+ |||||||||\n+Subject 2705 CCGTCGTGA 2713</pre>\n+ </div>\n+\n+ </div>\n+\n <div class=alignment id=hit1-36>\n \n <div class=linkheader>\n'