Repository 'ncbi_blast_plus'
hg clone https://testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus

Changeset 3:cf4903f5c81f (2013-04-17)
Previous changeset 2:b70b142bbc39 (2013-04-17) Next changeset 4:4afb12181d1a (2013-04-17)
Commit message:
Uploaded v0.0.17
modified:
test-data/blastp_four_human_vs_rhodopsin.tabular
test-data/blastp_four_human_vs_rhodopsin.xml
test-data/blastp_four_human_vs_rhodopsin_ext.tabular
test-data/blastp_rhodopsin_vs_four_human.tabular
test-data/blastx_rhodopsin_vs_four_human.tabular
test-data/blastx_rhodopsin_vs_four_human.xml
test-data/blastx_rhodopsin_vs_four_human_ext.tabular
test-data/tblastn_four_human_vs_rhodopsin.html
test-data/tblastn_four_human_vs_rhodopsin.tabular
test-data/tblastn_four_human_vs_rhodopsin.xml
test-data/tblastn_four_human_vs_rhodopsin_ext.tabular
tools/ncbi_blast_plus/blastxml_to_tabular.xml
tools/ncbi_blast_plus/ncbi_blast_plus.txt
tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
removed:
test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastp_four_human_vs_rhodopsin.tabular
--- a/test-data/blastp_four_human_vs_rhodopsin.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin.tabular Wed Apr 17 09:45:28 2013 -0400
b
@@ -3,4 +3,4 @@
 sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0  653
 sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0  631
 sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0  673
-sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 3e-176  599
+sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0  599
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastp_four_human_vs_rhodopsin.xml
--- a/test-data/blastp_four_human_vs_rhodopsin.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin.xml Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastp</BlastOutput_program>
-  <BlastOutput_version>BLASTP 2.2.25+</BlastOutput_version>
+  <BlastOutput_version>BLASTP 2.2.26+</BlastOutput_version>
   <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
   <BlastOutput_db></BlastOutput_db>
   <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID>
@@ -375,7 +375,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>701.049065538619</Hsp_bit-score>
+              <Hsp_bit-score>701.049</Hsp_bit-score>
               <Hsp_score>1808</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -422,7 +422,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>619.001555868222</Hsp_bit-score>
+              <Hsp_bit-score>619.002</Hsp_bit-score>
               <Hsp_score>1595</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -469,7 +469,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>653.284318124867</Hsp_bit-score>
+              <Hsp_bit-score>653.284</Hsp_bit-score>
               <Hsp_score>1684</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>11</Hsp_query-from>
@@ -516,7 +516,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>631.327942297578</Hsp_bit-score>
+              <Hsp_bit-score>631.328</Hsp_bit-score>
               <Hsp_score>1627</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>11</Hsp_query-from>
@@ -563,7 +563,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>673.314696072569</Hsp_bit-score>
+              <Hsp_bit-score>673.315</Hsp_bit-score>
               <Hsp_score>1736</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -610,9 +610,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>599.356377496438</Hsp_bit-score>
+              <Hsp_bit-score>599.356</Hsp_bit-score>
               <Hsp_score>1544</Hsp_score>
-              <Hsp_evalue>3.49521227372659e-176</Hsp_evalue>
+              <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
               <Hsp_query-to>341</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
@@ -643,4 +643,4 @@
       </Iteration_stat>
     </Iteration>
   </BlastOutput_iterations>
-</BlastOutput>
+</BlastOutput>
\ No newline at end of file
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastp_four_human_vs_rhodopsin_ext.tabular
--- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Wed Apr 17 09:45:28 2013 -0400
b
@@ -3,4 +3,4 @@
 sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0  653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328
 sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0  631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328
 sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0  673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347
-sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 3e-176  599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354
+sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0  599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastp_rhodopsin_vs_four_human.tabular
--- a/test-data/blastp_rhodopsin_vs_four_human.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastp_rhodopsin_vs_four_human.tabular Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,6 +1,6 @@
 gi|57163783|ref|NP_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 348 1 348 0.0  679
-gi|3024260|sp|P56514.1|OPSD_BUFBU sp|P08100|OPSD_HUMAN 83.33 354 53 2 1 354 1 348 6e-178  605
+gi|3024260|sp|P56514.1|OPSD_BUFBU sp|P08100|OPSD_HUMAN 83.33 354 53 2 1 354 1 348 0.0  605
 gi|283855846|gb|ADB45242.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0  630
 gi|283855823|gb|ADB45229.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0  630
 gi|223523|prf||0811197A sp|P08100|OPSD_HUMAN 93.10 348 23 1 1 347 1 348 0.0  651
-gi|12583665|dbj|BAB21486.1| sp|P08100|OPSD_HUMAN 81.09 349 65 1 1 349 1 348 2e-172  587
+gi|12583665|dbj|BAB21486.1| sp|P08100|OPSD_HUMAN 81.09 349 65 1 1 349 1 348 0.0  587
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastx_rhodopsin_vs_four_human.tabular
--- a/test-data/blastx_rhodopsin_vs_four_human.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastx_rhodopsin_vs_four_human.tabular Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,10 +1,10 @@
 gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0  662
-gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 1e-168  575
-gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-62  224
-gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-34  129
-gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 2e-31  120
-gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-30  118
-gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 6e-12 56.2
-gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 2e-180  613
+gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0  575
+gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68  224
+gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36  129
+gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33  120
+gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32  118
+gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2
+gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0  613
 gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0  641
-gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 6e-164  559
+gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0  559
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastx_rhodopsin_vs_four_human.xml
--- a/test-data/blastx_rhodopsin_vs_four_human.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastx_rhodopsin_vs_four_human.xml Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastx</BlastOutput_program>
-  <BlastOutput_version>BLASTX 2.2.25+</BlastOutput_version>
+  <BlastOutput_version>BLASTX 2.2.26+</BlastOutput_version>
   <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
   <BlastOutput_db></BlastOutput_db>
   <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
@@ -90,7 +90,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>662.143908370966</Hsp_bit-score>
+              <Hsp_bit-score>662.144</Hsp_bit-score>
               <Hsp_score>1707</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -194,9 +194,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>575.088804213644</Hsp_bit-score>
+              <Hsp_bit-score>575.089</Hsp_bit-score>
               <Hsp_score>1481</Hsp_score>
-              <Hsp_evalue>1.31349806431671e-168</Hsp_evalue>
+              <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>42</Hsp_query-from>
               <Hsp_query-to>1037</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
@@ -298,9 +298,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>224.171990552935</Hsp_bit-score>
+              <Hsp_bit-score>224.172</Hsp_bit-score>
               <Hsp_score>570</Hsp_score>
-              <Hsp_evalue>1.57574304751949e-62</Hsp_evalue>
+              <Hsp_evalue>1.84906e-68</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
               <Hsp_query-to>333</Hsp_query-to>
               <Hsp_hit-from>11</Hsp_hit-from>
@@ -317,9 +317,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>129.412894877266</Hsp_bit-score>
+              <Hsp_bit-score>129.413</Hsp_bit-score>
               <Hsp_score>324</Hsp_score>
-              <Hsp_evalue>5.28220874623366e-34</Hsp_evalue>
+              <Hsp_evalue>4.62305e-36</Hsp_evalue>
               <Hsp_query-from>3174</Hsp_query-from>
               <Hsp_query-to>3368</Hsp_query-to>
               <Hsp_hit-from>248</Hsp_hit-from>
@@ -336,9 +336,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>120.938504207085</Hsp_bit-score>
+              <Hsp_bit-score>120.939</Hsp_bit-score>
               <Hsp_score>302</Hsp_score>
-              <Hsp_evalue>1.87871691987854e-31</Hsp_evalue>
+              <Hsp_evalue>2.85192e-33</Hsp_evalue>
               <Hsp_query-from>2855</Hsp_query-from>
               <Hsp_query-to>3022</Hsp_query-to>
               <Hsp_hit-from>177</Hsp_hit-from>
@@ -355,9 +355,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>118.242107175663</Hsp_bit-score>
+              <Hsp_bit-score>118.242</Hsp_bit-score>
               <Hsp_score>295</Hsp_score>
-              <Hsp_evalue>1.21774886471054e-30</Hsp_evalue>
+              <Hsp_evalue>2.16231e-32</Hsp_evalue>
               <Hsp_query-from>1404</Hsp_query-from>
               <Hsp_query-to>1580</Hsp_query-to>
               <Hsp_hit-from>119</Hsp_hit-from>
@@ -374,9 +374,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>56.2249754529693</Hsp_bit-score>
+              <Hsp_bit-score>56.225</Hsp_bit-score>
               <Hsp_score>134</Hsp_score>
-              <Hsp_evalue>5.68296036241677e-12</Hsp_evalue>
+              <Hsp_evalue>2.05678e-12</Hsp_evalue>
               <Hsp_query-from>4222</Hsp_query-from>
               <Hsp_query-to>4296</Hsp_query-to>
               <Hsp_hit-from>312</Hsp_hit-from>
@@ -478,9 +478,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>613.993961381297</Hsp_bit-score>
+              <Hsp_bit-score>613.994</Hsp_bit-score>
               <Hsp_score>1582</Hsp_score>
-              <Hsp_evalue>1.57028732393616e-180</Hsp_evalue>
+              <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
               <Hsp_query-to>978</Hsp_query-to>
               <Hsp_hit-from>11</Hsp_hit-from>
@@ -582,7 +582,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>641.728330847346</Hsp_bit-score>
+              <Hsp_bit-score>641.728</Hsp_bit-score>
               <Hsp_score>1654</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -686,9 +686,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>559.295621601033</Hsp_bit-score>
+              <Hsp_bit-score>559.296</Hsp_bit-score>
               <Hsp_score>1440</Hsp_score>
-              <Hsp_evalue>6.32632556748138e-164</Hsp_evalue>
+              <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>23</Hsp_query-from>
               <Hsp_query-to>1018</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
@@ -719,4 +719,4 @@
       </Iteration_stat>
     </Iteration>
   </BlastOutput_iterations>
-</BlastOutput>
+</BlastOutput>
\ No newline at end of file
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastx_rhodopsin_vs_four_human_ext.tabular
--- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Wed Apr 17 09:45:28 2013 -0400
b
b'@@ -1,10 +1,10 @@\n gi|57163782|ref|NM_001009242.1|\tsp|P08100|OPSD_HUMAN\t96.55\t348\t12\t0\t1\t1044\t1\t348\t0.0\t 662\tsp|P08100|OPSD_HUMAN\t1707\t336\t343\t0\t98.56\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n-gi|2734705|gb|U59921.1|BBU59921\tsp|P08100|OPSD_HUMAN\t85.24\t332\t49\t0\t42\t1037\t1\t332\t1e-168\t 575\tsp|P08100|OPSD_HUMAN\t1481\t283\t315\t0\t94.88\t3\t0\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t2e-62\t 224\tsp|P08100|OPSD_HUMAN\t570\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t5e-34\t 129\tsp|P08100|OPSD_HUMAN\t324\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.43\t56\t2\t0\t2855\t3022\t177\t232\t2e-31\t 120\tsp|P08100|OPSD_HUMAN\t302\t54\t56\t0\t100.00\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t1e-30\t 118\tsp|P08100|OPSD_HUMAN\t295\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.00\t25\t2\t0\t4222\t4296\t312\t336\t6e-12\t56.2\tsp|P08100|OPSD_HUMAN\t134\t23\t24\t0\t96.00\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTT\tQFRNCMLTTICCGKNPLGDDEASAT\t4301\t348\n-gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t2e-180\t 613\tsp|P08100|OPSD_HUMAN\t1582\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n+gi|2734705|gb|U59921.1|BBU59921\tsp|P08100|OPSD_HUMAN\t85.24\t332\t49\t0\t42\t1037\t1\t332\t0.0\t 575\tsp|P08100|OPSD_HUMAN\t1481\t283\t315\t0\t94.88\t3\t0\tMNGTEGPNFYIPMSNKTGVVRSPF'..b'AIYNPVIYIMMNKQ\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.43\t56\t2\t0\t2855\t3022\t177\t232\t3e-33\t 120\tsp|P08100|OPSD_HUMAN\t302\t54\t56\t0\t100.00\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t2e-32\t 118\tsp|P08100|OPSD_HUMAN\t295\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.00\t25\t2\t0\t4222\t4296\t312\t336\t2e-12\t56.2\tsp|P08100|OPSD_HUMAN\t134\t23\t24\t0\t96.00\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTT\tQFRNCMLTTICCGKNPLGDDEASAT\t4301\t348\n+gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t 613\tsp|P08100|OPSD_HUMAN\t1582\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\n gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t 641\tsp|P08100|OPSD_HUMAN\t1654\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\n-gi|12583664|dbj|AB043817.1|\tsp|P08100|OPSD_HUMAN\t81.93\t332\t60\t0\t23\t1018\t1\t332\t6e-164\t 559\tsp|P08100|OPSD_HUMAN\t1440\t272\t307\t0\t92.47\t2\t0\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1344\t348\n+gi|12583664|dbj|AB043817.1|\tsp|P08100|OPSD_HUMAN\t81.93\t332\t60\t0\t23\t1018\t1\t332\t0.0\t 559\tsp|P08100|OPSD_HUMAN\t1440\t272\t307\t0\t92.47\t2\t0\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1344\t348\n'
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin.html
--- a/test-data/tblastn_four_human_vs_rhodopsin.html Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.html Wed Apr 17 09:45:28 2013 -0400
b
@@ -3,7 +3,7 @@
 <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
 <PRE>
 
-<b>TBLASTN 2.2.25+</b>
+<b>TBLASTN 2.2.26+</b>
 
 
 <b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
@@ -563,7 +563,7 @@
 
 <script src="blastResult.js"></script>
  Score =  151 bits (342),  Expect(2) = 1e-72, Method: Compositional matrix adjust.
- Identities = 69/74 (94%), Positives = 73/74 (99%), Gaps = 0/74 (0%)
+ Identities = 69/74 (93%), Positives = 73/74 (99%), Gaps = 0/74 (0%)
  Frame = +3
 
 Query  239   ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA  298
@@ -584,8 +584,8 @@
 Sbjct  2855  RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS  3031
 
 
- Score =  229 bits (523),  Expect = 1e-64, Method: Compositional matrix adjust.
- Identities = 107/111 (97%), Positives = 109/111 (99%), Gaps = 0/111 (0%)
+ Score =  229 bits (523),  Expect = 9e-67, Method: Compositional matrix adjust.
+ Identities = 107/111 (96%), Positives = 109/111 (98%), Gaps = 0/111 (0%)
  Frame = +1
 
 Query  11   VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  70
@@ -598,7 +598,7 @@
 
 
  Score =  122 bits (276),  Expect = 1e-32, Method: Compositional matrix adjust.
- Identities = 55/59 (94%), Positives = 56/59 (95%), Gaps = 0/59 (0%)
+ Identities = 55/59 (93%), Positives = 56/59 (95%), Gaps = 0/59 (0%)
  Frame = +3
 
 Query  119   LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR  177
@@ -606,8 +606,8 @@
 Sbjct  1404  LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR  1580
 
 
- Score = 57.7 bits (125),  Expect = 6e-13, Method: Compositional matrix adjust.
- Identities = 23/26 (89%), Positives = 24/26 (93%), Gaps = 0/26 (0%)
+ Score = 57.7 bits (125),  Expect = 2e-12, Method: Compositional matrix adjust.
+ Identities = 23/26 (88%), Positives = 24/26 (92%), Gaps = 0/26 (0%)
  Frame = +1
 
 Query  312   QFRNCMLTTICCGKNPLGDDEASATV  337
@@ -637,7 +637,7 @@
 
 <script src="blastResult.js"></script>
  Score =  658 bits (1517),  Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 310/326 (96%), Positives = 322/326 (99%), Gaps = 0/326 (0%)
+ Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%)
  Frame = +1
 
 Query  11   VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  70
@@ -687,7 +687,7 @@
 
 <script src="blastResult.js"></script>
  Score =  711 bits (1640),  Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 325/348 (94%), Positives = 337/348 (97%), Gaps = 0/348 (0%)
+ Identities = 325/348 (93%), Positives = 337/348 (97%), Gaps = 0/348 (0%)
  Frame = +1
 
 Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
@@ -737,7 +737,7 @@
 
 <script src="blastResult.js"></script>
  Score =  626 bits (1444),  Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 281/342 (83%), Positives = 311/342 (91%), Gaps = 1/342 (0%)
+ Identities = 281/342 (82%), Positives = 311/342 (91%), Gaps = 1/342 (0%)
  Frame = +2
 
 Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.tabular Wed Apr 17 09:45:28 2013 -0400
b
@@ -2,9 +2,9 @@
 sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0  646
 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72  151
 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72  126
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64  229
+sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67  229
 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32  122
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7
+sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7
 sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0  658
 sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0  711
 sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0  626
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin.xml
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>tblastn</BlastOutput_program>
-  <BlastOutput_version>TBLASTN 2.2.25+</BlastOutput_version>
+  <BlastOutput_version>TBLASTN 2.2.26+</BlastOutput_version>
   <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
   <BlastOutput_db></BlastOutput_db>
   <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
@@ -375,7 +375,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>732.392902459534</Hsp_bit-score>
+              <Hsp_bit-score>732.393</Hsp_bit-score>
               <Hsp_score>1689</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -422,7 +422,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>646.119739014374</Hsp_bit-score>
+              <Hsp_bit-score>646.12</Hsp_bit-score>
               <Hsp_score>1489</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -469,9 +469,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>151.343146656381</Hsp_bit-score>
+              <Hsp_bit-score>151.343</Hsp_bit-score>
               <Hsp_score>342</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
+              <Hsp_evalue>1.39567e-72</Hsp_evalue>
               <Hsp_query-from>239</Hsp_query-from>
               <Hsp_query-to>312</Hsp_query-to>
               <Hsp_hit-from>3147</Hsp_hit-from>
@@ -488,9 +488,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>126.323929257285</Hsp_bit-score>
+              <Hsp_bit-score>126.324</Hsp_bit-score>
               <Hsp_score>284</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
+              <Hsp_evalue>1.39567e-72</Hsp_evalue>
               <Hsp_query-from>177</Hsp_query-from>
               <Hsp_query-to>235</Hsp_query-to>
               <Hsp_hit-from>2855</Hsp_hit-from>
@@ -507,9 +507,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>229.420359574251</Hsp_bit-score>
+              <Hsp_bit-score>229.42</Hsp_bit-score>
               <Hsp_score>523</Hsp_score>
-              <Hsp_evalue>9.84654801241353e-65</Hsp_evalue>
+              <Hsp_evalue>9.34154e-67</Hsp_evalue>
               <Hsp_query-from>11</Hsp_query-from>
               <Hsp_query-to>121</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
@@ -526,9 +526,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>122.873002719478</Hsp_bit-score>
+              <Hsp_bit-score>122.873</Hsp_bit-score>
               <Hsp_score>276</Hsp_score>
-              <Hsp_evalue>1.40732096096596e-32</Hsp_evalue>
+              <Hsp_evalue>1.03783e-32</Hsp_evalue>
               <Hsp_query-from>119</Hsp_query-from>
               <Hsp_query-to>177</Hsp_query-to>
               <Hsp_hit-from>1404</Hsp_hit-from>
@@ -545,9 +545,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>57.7367643183824</Hsp_bit-score>
+              <Hsp_bit-score>57.7368</Hsp_bit-score>
               <Hsp_score>125</Hsp_score>
-              <Hsp_evalue>5.60065526485586e-13</Hsp_evalue>
+              <Hsp_evalue>1.50808e-12</Hsp_evalue>
               <Hsp_query-from>312</Hsp_query-from>
               <Hsp_query-to>337</Hsp_query-to>
               <Hsp_hit-from>4222</Hsp_hit-from>
@@ -592,7 +592,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>658.197981896696</Hsp_bit-score>
+              <Hsp_bit-score>658.198</Hsp_bit-score>
               <Hsp_score>1517</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>11</Hsp_query-from>
@@ -639,7 +639,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>711.255977415469</Hsp_bit-score>
+              <Hsp_bit-score>711.256</Hsp_bit-score>
               <Hsp_score>1640</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -686,7 +686,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>626.708277239213</Hsp_bit-score>
+              <Hsp_bit-score>626.708</Hsp_bit-score>
               <Hsp_score>1444</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -719,4 +719,4 @@
       </Iteration_stat>
     </Iteration>
   </BlastOutput_iterations>
-</BlastOutput>
+</BlastOutput>
\ No newline at end of file
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin_ext.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Wed Apr 17 09:45:28 2013 -0400
b
@@ -2,9 +2,9 @@
 sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0  646 gi|2734705|gb|U59921.1|BBU59921 1489 290 320 1 93.57 0 3 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 1574
 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72  151 gi|283855845|gb|GQ290303.1| 342 69 73 0 98.65 0 3 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 348 4301
 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72  126 gi|283855845|gb|GQ290303.1| 284 54 57 0 96.61 0 2 RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 348 4301
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64  229 gi|283855845|gb|GQ290303.1| 523 107 109 0 98.20 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 348 4301
+sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67  229 gi|283855845|gb|GQ290303.1| 523 107 109 0 98.20 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 348 4301
 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32  122 gi|283855845|gb|GQ290303.1| 276 55 56 0 94.92 0 3 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 348 4301
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7 gi|283855845|gb|GQ290303.1| 125 23 24 0 92.31 0 1 QFRNCMLTTICCGKNPLGDDEASATV QFRNCMLTTLCCGKNPLGDDEASTTA 348 4301
+sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7 gi|283855845|gb|GQ290303.1| 125 23 24 0 92.31 0 1 QFRNCMLTTICCGKNPLGDDEASATV QFRNCMLTTLCCGKNPLGDDEASTTA 348 4301
 sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0  658 gi|283855822|gb|GQ290312.1| 1517 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983
 sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0  711 gi|18148870|dbj|AB062417.1| 1640 325 337 0 96.84 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 1047
 sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0  626 gi|12583664|dbj|AB043817.1| 1444 281 311 1 90.94 0 2 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 1344
b
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular Wed Apr 17 09:44:44 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,10 +0,0 @@
-sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.55 348 12 0 1 348 1 1044 0.0  732
-sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0  646
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72  151
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72  126
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64  229
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32  122
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7
-sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0  658
-sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0  711
-sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0  626
b
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,13 +1,18 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8">
+<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.10">
     <description>Convert BLAST XML output to tabular</description>
     <command interpreter="python">
       blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
     </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <inputs>
         <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> 
         <param name="out_format" type="select" label="Output format">
-            <option value="std" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
+            <option value="std">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
         </param>
     </inputs>
     <outputs>
@@ -74,7 +79,7 @@
 may need both the XML and the tabular output - but running BLAST twice is
 slow and wasteful.
 
-This tool takes the BLAST XML output and by default converts it into the
+This tool takes the BLAST XML output and can convert it into the
 standard 12 column tabular equivalent:
 
 ====== ========= ============================================
@@ -99,7 +104,7 @@
 included by selecting the extended tabular output. The extra columns are
 included *after* the standard 12 columns. This is so that you can write
 workflow filtering steps that accept either the 12 or 22 column tabular
-BLAST output.
+BLAST output. This tool now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
@@ -121,7 +126,7 @@
 Beware that the XML file (and thus the conversion) and the tabular output
 direct from BLAST+ may differ in the presence of XXXX masking on regions
 low complexity (columns 21 and 22), and thus also calculated figures like
-the percentage idenity (column 3).
+the percentage identity (column 3).
 
     </help>
 </tool>
b
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_blast_plus.txt
--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt Wed Apr 17 09:45:28 2013 -0400
b
@@ -34,7 +34,20 @@
 
 For those not using Galaxy's automated installation from the Tool Shed, put
 the XML and Python files under tools/ncbi_blast_plus and add the XML files
-to your tool_conf.xml as normal.
+to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample
+in order to run the unit tests). For example, use:
+
+  <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
+    <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" />
+    <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
+  </section>
 
 You will also need to install 'blast_datatypes' from the Tool Shed. This
 defines the BLAST XML file format ('blastxml') and protein and nucleotide
@@ -45,6 +58,14 @@
 databases like NR), located in the tool-data folder. Sample fils are included
 which explain the tab based format to use.
 
+You must install the NCBI BLAST+ standalone tools somewhere on the system
+path. Currently the unit tests are written using "BLAST 2.2.26+".
+
+Run the functional tests (adusting the section identifier to match your
+tool_conf.xml.sample file):
+
+./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools
+
 
 History
 =======
@@ -65,6 +86,9 @@
           FASTA files (better looking e-values than you might be expecting).
 v0.0.16 - Added repository_dependencies.xml for automates installation of the
           'blast_datatypes' repository from the Tool Shed.
+v0.0.17 - The BLAST+ search tools now default to extended tabular output
+          (all too often our users where having to re-run searches just to
+          get one of the missing columns like query or subject length)
 
 
 Developers
b
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.15">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.17">
     <description>Search nucleotide database with nucleotide query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
@@ -91,8 +91,8 @@
         </param>
         <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
         <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
+            <option value="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -200,7 +200,7 @@
 included by selecting the extended tabular output. The extra columns are
 included *after* the standard 12 columns. This is so that you can write
 workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
b
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.15">
+<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.17">
     <description>Search protein database with protein query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
@@ -86,8 +86,8 @@
         </param>
         <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
         <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
+            <option value="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -265,7 +265,7 @@
 included by selecting the extended tabular output. The extra columns are
 included *after* the standard 12 columns. This is so that you can write
 workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
b
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.15">
+<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.17">
     <description>Search protein database with translated nucleotide query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
@@ -103,8 +103,8 @@
         </param>
         <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
         <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
+            <option value="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -253,7 +253,7 @@
 included by selecting the extended tabular output. The extra columns are
 included *after* the standard 12 columns. This is so that you can write
 workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
b
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.15">
+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.17">
     <description>Search translated nucleotide database with protein query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
@@ -82,8 +82,8 @@
         </conditional>
         <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
         <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
+            <option value="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -216,7 +216,7 @@
             <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
         </test>
         <test>
-            <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference -->
+            <!-- Same as above, but parse deflines - on BLAST 2.2.25+ - 2.2.27+ makes no difference -->
             <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
             <param name="db_opts_selector" value="file" />
             <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
@@ -299,7 +299,7 @@
 included by selecting the extended tabular output. The extra columns are
 included *after* the standard 12 columns. This is so that you can write
 workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
b
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
b
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.15">
+<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.17">
     <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
@@ -103,8 +103,8 @@
         </param>
         <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
         <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
+            <option value="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -241,7 +241,7 @@
 included by selecting the extended tabular output. The extra columns are
 included *after* the standard 12 columns. This is so that you can write
 workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description