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changeset 52:fa7f92b81db1 draft

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"Updated to 2.9.0+galaxy0"
author peterjc
date Thu, 10 Sep 2020 10:32:26 +0000
parents 1ebae91eb6e9
children 061c2abccfea
files test-data/blastn_chimera_vs_three_human_max1.txt test-data/blastn_rhodopsin_vs_three_human.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastx_rhodopsin_vs_four_human.xml test-data/cd00003_and_cd00008.pin test-data/four_human_proteins.fasta.pin test-data/four_human_proteins_taxid.fasta.pin test-data/rhodopsin_nucs.fasta.nin test-data/tblastn_four_human_vs_rhodopsin.html test-data/tblastn_four_human_vs_rhodopsin.xml test-data/three_human_mRNA.fasta.nin tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml
diffstat 14 files changed, 25 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/blastn_chimera_vs_three_human_max1.txt	Wed Sep 09 14:32:53 2020 +0000
+++ b/test-data/blastn_chimera_vs_three_human_max1.txt	Thu Sep 10 10:32:26 2020 +0000
@@ -1,4 +1,4 @@
-BLASTN 2.7.1+
+BLASTN 2.9.0+
 
 
 Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
@@ -15,13 +15,13 @@
 Query= chimera chunks of AB011145 plus M10051 plus BC112106
 
 Length=9973
-                                                                      Score     E
-Sequences producing significant alignments:                          (Bits)  Value
+                                                                      Score        E
+Sequences producing significant alignments:                          (Bits)     Value
 
-  ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein,...  8421    0.0  
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, p...  8421       0.0  
 
 
-> ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, 
+>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, 
 partial cds.
 Length=4796
 
@@ -346,7 +346,7 @@
 
 
   Database: Just 3 human mRNA sequences
-    Posted date:  Oct 31, 2017  4:23 PM
+    Posted date:  Apr 23, 2020  3:16 PM
   Number of letters in database: 10,732
   Number of sequences in database:  3
 
--- a/test-data/blastn_rhodopsin_vs_three_human.xml	Wed Sep 09 14:32:53 2020 +0000
+++ b/test-data/blastn_rhodopsin_vs_three_human.xml	Thu Sep 10 10:32:26 2020 +0000
@@ -2,7 +2,7 @@
 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastn</BlastOutput_program>
-  <BlastOutput_version>BLASTN 2.7.1+</BlastOutput_version>
+  <BlastOutput_version>BLASTN 2.9.0+</BlastOutput_version>
   <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), &quot;A greedy algorithm for aligning DNA sequences&quot;, J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference>
   <BlastOutput_db></BlastOutput_db>
   <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
--- a/test-data/blastp_four_human_vs_rhodopsin.xml	Wed Sep 09 14:32:53 2020 +0000
+++ b/test-data/blastp_four_human_vs_rhodopsin.xml	Thu Sep 10 10:32:26 2020 +0000
@@ -2,7 +2,7 @@
 <!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 2.7.1+</BlastOutput_version>
+  <BlastOutput_version>BLASTP 2.9.0+</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>Q9BS26</BlastOutput_query-ID>
--- a/test-data/blastx_rhodopsin_vs_four_human.xml	Wed Sep 09 14:32:53 2020 +0000
+++ b/test-data/blastx_rhodopsin_vs_four_human.xml	Thu Sep 10 10:32:26 2020 +0000
@@ -2,7 +2,7 @@
 <!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 2.7.1+</BlastOutput_version>
+  <BlastOutput_version>BLASTX 2.9.0+</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>
Binary file test-data/cd00003_and_cd00008.pin has changed
Binary file test-data/four_human_proteins.fasta.pin has changed
Binary file test-data/four_human_proteins_taxid.fasta.pin has changed
Binary file test-data/rhodopsin_nucs.fasta.nin has changed
--- a/test-data/tblastn_four_human_vs_rhodopsin.html	Wed Sep 09 14:32:53 2020 +0000
+++ b/test-data/tblastn_four_human_vs_rhodopsin.html	Thu Sep 10 10:32:26 2020 +0000
@@ -3,7 +3,7 @@
 <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
 <PRE>
 
-<b>TBLASTN 2.7.1+</b>
+<b>TBLASTN 2.9.0+</b>
 
 
 <b><a
@@ -84,15 +84,15 @@
 <b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
 
 Length=348
-                                                                      Score     E
-Sequences producing significant alignments:                          (Bits)  Value
+                                                                      Score        E
+Sequences producing significant alignments:                          (Bits)     Value
 
-  gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA   <a href=#Subject_1>732</a>     0.0  
-  gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene...  <a href=#Subject_5>711</a>     0.0  
-  gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodo...  <a href=#Subject_4>658</a>     0.0  
-  gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, compl...  <a href=#Subject_2>646</a>     0.0  
-  gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fres...  <a href=#Subject_6>626</a>     0.0  
-  gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020...  <a href=#Subject_3>151</a>     1e-71
+gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA     <a href=#Subject_1>732</a>        0.0  
+gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene f...  <a href=#Subject_5>711</a>        0.0  
+gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodops...  <a href=#Subject_4>658</a>        0.0  
+gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complet...  <a href=#Subject_2>646</a>        0.0  
+gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh ...  <a href=#Subject_6>626</a>        0.0  
+gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 2002043...  <a href=#Subject_3>229</a>        3e-67
 
 
 ><a name=Subject_1></a> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), 
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml	Wed Sep 09 14:32:53 2020 +0000
+++ b/test-data/tblastn_four_human_vs_rhodopsin.xml	Thu Sep 10 10:32:26 2020 +0000
@@ -2,7 +2,7 @@
 <!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 2.7.1+</BlastOutput_version>
+  <BlastOutput_version>TBLASTN 2.9.0+</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>
Binary file test-data/three_human_mRNA.fasta.nin has changed
--- a/tools/ncbi_blast_plus/README.rst	Wed Sep 09 14:32:53 2020 +0000
+++ b/tools/ncbi_blast_plus/README.rst	Thu Sep 10 10:32:26 2020 +0000
@@ -3,8 +3,8 @@
 
 These wrappers are copyright 2010-2018 by Peter Cock (James Hutton Institute,
 UK) and additional contributors including Edward Kirton, John Chilton, Nicola
-Soranzo, Jim Johnson, Bjoern Gruening, Caleb Easterly, and Anton Nekrutenko.
-See the licence text below.
+Soranzo, Jim Johnson, Bjoern Gruening, Caleb Easterly, Anton Nekrutenko and
+Anthony Bretaudeau. See the licence text below.
 
 Note this does not work with the NCBI 'legacy' BLAST suite written in C
 (e.g. binary name ``blastall``), but its replacement BLAST, which is
@@ -136,6 +136,8 @@
 ============== ===============================================================
 Version        Changes
 -------------- ---------------------------------------------------------------
+2.9.0+galaxy0  - Updated for NCBI BLAST+ 2.9.0 release (contribution from
+                 Anthony Bretaudeau).
 2.7.1+galaxy0  - Adopted BLAST version with integer Galaxy wrapper suffix.
                - Dropped legacy ``repository_dependencies.xml`` and
                  ``tool_dependencies.xml`` files. Instead assumes conda for
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Wed Sep 09 14:32:53 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Thu Sep 10 10:32:26 2020 +0000
@@ -98,7 +98,7 @@
             <param name="id_opts|id_type" value="file" />
             <param name="id_opts|entries" value="rhodopsin_nucs.blastdbcmd.txt" ftype="txt" />
             <param name="outfmt" value="original" />
-            <output name="seq" file="rhodopsin_nucs.no_gi.fasta" ftype="fasta" />
+            <output name="seq" file="rhodopsin_nucs.no_gi.region.fasta" ftype="fasta" />
         </test>
         <test>
             <param name="db_opts|db_type" value="nucl" />
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Wed Sep 09 14:32:53 2020 +0000
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Thu Sep 10 10:32:26 2020 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.7.1</token>
+    <token name="@TOOL_VERSION@">2.9.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">16.10</token>
     <xml name="parallelism">