| Previous changeset 97:8b3c5d334a84 (2014-06-30) Next changeset 99:8f02008a5f20 (2014-07-01) |
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Commit message:
test new command line parameters, fix small bug |
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modified:
blast2html.py test-data/blast xml example3.html test-data/blast xml example4.html test-data/refresh_test_results.sh |
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added:
test-data/blastdb.loc |
| b |
| diff -r 8b3c5d334a84 -r e780606b7c25 blast2html.py --- a/blast2html.py Mon Jun 30 17:31:26 2014 +0200 +++ b/blast2html.py Mon Jun 30 17:51:56 2014 +0200 |
| [ |
| @@ -386,7 +386,7 @@ for l in f.readlines(): if l.strip().startswith('#'): continue - line = l.split('\t') + line = l.rstrip('\n').split('\t') try: links[line[2]] = line[3] except IndexError: |
| b |
| diff -r 8b3c5d334a84 -r e780606b7c25 test-data/blast xml example3.html --- a/test-data/blast xml example3.html Mon Jun 30 17:31:26 2014 +0200 +++ b/test-data/blast xml example3.html Mon Jun 30 17:51:56 2014 +0200 |
| b |
| b'@@ -794,7 +794,7 @@\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$=nuclalign">Subject_3</a></td>\n+ <td><a href="http://example.com/example-genebank?id=Subject_3">Subject_3</a></td>\n </tr>\n </table>\n \n@@ -811,13 +811,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description3-1">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" 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://www.ncbi.nlm.nih.gov/nucleotide/Subject_3?report=genbank&log$=nuclalign">Subject_3</a>\n+ <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_3">Subject_3</a>\n <span class=b>Length:</span> 323\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -1030,7 +1030,7 @@\n <td>100%</td>\n <td>7.011e-08</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Subject_6</a></td>\n+ <td><a href="http://example.com/example-genebank?id=Subject_6">Subject_6</a></td>\n </tr>\n </table>\n \n@@ -1047,13 +1047,13 @@\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/nucleotide/Subject_6?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" href="http://example.com/example-genebank?id=Subject_6">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_6?report=genbank&log$=nuclalign">Subject_6</a>\n+ <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_6">Subject_6</a>\n <span class=b>Length:</span> 2457\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -1502,7 +1502,7 @@\n <td>85%</td>\n <td>2.981e-06</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_2?report=genbank&log$=nuclalign">Subject_2</a></td>\n+ <td><a href="http://example.com/example-genebank?id=Subject_2">Subject_2</a></td>\n </tr>\n </table>\n \n@@ -1519,13 +1519,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description18-1">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_2?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" href="http://example.com/example-genebank?id=Subject_2">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>AJ308515.1|GenBank|insert_GTS-40-3-2|Synt'..b' @@\n \n <div class=linkheader>\n <div class=right><a href="#description48-1">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" href="http://example.com/example-genebank?id=Subject_8">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a>\n+ <span class=b>Sequence ID:</span> <a 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@@ -3249,7 +3249,7 @@\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_7?report=genbank&log$=nuclalign">Subject_7</a></td>\n+ <td><a href="http://example.com/example-genebank?id=Subject_7">Subject_7</a></td>\n </tr>\n </table>\n \n@@ -3266,13 +3266,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description55-1">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" 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://www.ncbi.nlm.nih.gov/nucleotide/Subject_7?report=genbank&log$=nuclalign">Subject_7</a>\n+ <span class=b>Sequence ID:</span> <a href="http://example.com/example-genebank?id=Subject_7">Subject_7</a>\n <span class=b>Length:</span> 4180\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -3437,7 +3437,7 @@\n <td>100%</td>\n <td>6.629e-23</td>\n <td>86%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a></td>\n+ <td><a href="http://example.com/example-genebank?id=Subject_8">Subject_8</a></td>\n </tr>\n </table>\n \n@@ -3454,13 +3454,13 @@\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$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" href="http://example.com/example-genebank?id=Subject_8">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a>\n+ <span class=b>Sequence ID:</span> <a 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' |
| b |
| diff -r 8b3c5d334a84 -r e780606b7c25 test-data/blast xml example4.html --- a/test-data/blast xml example4.html Mon Jun 30 17:31:26 2014 +0200 +++ b/test-data/blast xml example4.html Mon Jun 30 17:51:56 2014 +0200 |
| b |
| b'@@ -557,7 +557,7 @@\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$=nuclalign">5</a></td>\n+ <td><a href="http://example.com/example-genebank/AB209952.1/">5</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit1-2"\n@@ -570,7 +570,7 @@\n <td>100%</td>\n <td>1.513e-07</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">2</a></td>\n+ <td><a href="http://example.com/example-genebank/DJ437711/">2</a></td>\n </tr>\n </table>\n \n@@ -587,13 +587,13 @@\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$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" href="http://example.com/example-genebank/AB209952.1/">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/5?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|5</a>\n+ <span class=b>Sequence ID:</span> <a 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@@ -629,13 +629,13 @@\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$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" href="http://example.com/example-genebank/DJ437711/">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|2</a>\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>Length:</span> 323\n <span class=b>Number of Matches:</span> 1\n </p>\n@@ -846,7 +846,7 @@\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$=nuclalign">5</a></td>\n+ <td><a href="http://example.com/example-genebank/AB209952.1/">5</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit3-2"\n@@ -859,7 +859,7 @@\n <td>100%</td>\n <td>1.513e-07</td>\n <td>100%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/2?report=genbank&log$=nuclalign">2</a></td>\n+ <td><a href="http://example.com/example-genebank/DJ437711/">2</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit3-3"\n@@ -872,7 +872,7 @@\n <td>85%</td>\n <td>9.334e-06</td>\n <td>100%</td>\n- '..b'+1276,13 @@\n \n <div class=linkheader>\n <div class=right><a href="#description6-2">Descriptions</a></div>\n- <a class="linkheader" href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" href="http://example.com/example-genebank/AY326434/">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|6</a>\n+ <span class=b>Sequence ID:</span> <a 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@@ -1455,7 +1455,7 @@\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/7?report=genbank&log$=nuclalign">7</a></td>\n+ <td><a href="http://example.com/example-genebank/EUG/">7</a></td>\n </tr>\n <tr>\n <td><div><a href="#hit7-2"\n@@ -1468,7 +1468,7 @@\n <td>100%</td>\n <td>3.564e-15</td>\n <td>86%</td>\n- <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">6</a></td>\n+ <td><a href="http://example.com/example-genebank/AY326434/">6</a></td>\n </tr>\n </table>\n \n@@ -1485,13 +1485,13 @@\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$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" href="http://example.com/example-genebank/EUG/">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/7?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|7</a>\n+ <span class=b>Sequence ID:</span> <a 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@@ -1530,13 +1530,13 @@\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$=nuclalign">Gene Bank</a>\n+ <a class="linkheader" href="http://example.com/example-genebank/AY326434/">Gene Bank</a>\n </div>\n \n <div class=title>\n <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p>\n <p class=titleinfo>\n- <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/6?report=genbank&log$=nuclalign">gnl|BL_ORD_ID|6</a>\n+ <span class=b>Sequence ID:</span> <a 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' |
| b |
| diff -r 8b3c5d334a84 -r e780606b7c25 test-data/blastdb.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb.loc Mon Jun 30 17:51:56 2014 +0200 |
| [ |
| @@ -0,0 +1,39 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of nucleotide BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): +# +#<unique_id> <database_caption> <base_name_path> +# +#The captions typically contain spaces and might end with the build date. +#It is important that the actual database name does not have a space in +#it, and that there are only two tabs on each line. +# +#So, for example, if your database is nt and the path to your base name +#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry +#would look like this: +# +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +# +#and your /depot/data2/galaxy/blastdb/nt directory would contain all of +#your "base names" (e.g.): +# +#-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr +#-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin +#-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq +#...etc... +# +#Your blastdb.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk +#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test +#...etc... +# +#You can download the NCBI provided protein databases like NT from here: +#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# +#See also blastdb_p.loc which is for any protein BLAST database, and +#blastdb_d.loc which is for any protein domains databases (like CDD). + +EUginius_plasmid Euginius plasmid insert /opt/galaxy/blastdbs/EUginius_plasmid_insert http://example.com/example-genebank/{defline[0]}/ |
| b |
| diff -r 8b3c5d334a84 -r e780606b7c25 test-data/refresh_test_results.sh --- a/test-data/refresh_test_results.sh Mon Jun 30 17:31:26 2014 +0200 +++ b/test-data/refresh_test_results.sh Mon Jun 30 17:51:56 2014 +0200 |
| b |
| @@ -4,7 +4,8 @@ set -eu -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 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 . + |