Mercurial > repos > peterjc > ncbi_blast_plus

changeset 37:72170c3f515a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.22f, fix for new style dummy IDs in BLAST XML output
author peterjc
date Tue, 03 Dec 2013 10:02:17 -0500
parents 8f9023b30384
children 2f7fac29bb3c
files test-data/blastn_arabidopsis.extended.tabular test-data/blastn_arabidopsis.standard.tabular test-data/blastn_arabidopsis.xml tools/ncbi_blast_plus/blastxml_to_tabular.py tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_macros.xml
diffstat 6 files changed, 96 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_arabidopsis.extended.tabular	Tue Dec 03 10:02:17 2013 -0500
@@ -0,0 +1,1 @@
+chunk_of_plant	chrIII	100.00	630	0	0	1	630	4341	4970	0.0	1164	chrIII	630	630	630	0	100.00	1	1	GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT	GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT	630	23459830	gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_arabidopsis.standard.tabular	Tue Dec 03 10:02:17 2013 -0500
@@ -0,0 +1,1 @@
+chunk_of_plant	chrIII	100.00	630	0	0	1	630	4341	4970	0.0	1164
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_arabidopsis.xml	Tue Dec 03 10:02:17 2013 -0500
@@ -0,0 +1,71 @@
+<?xml version="1.0"?>
+<!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 2.2.28+</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>/mnt/galaxy/galaxy-central/database/files/000/dataset_857_files/blastdb</BlastOutput_db>
+  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
+  <BlastOutput_query-def>chunk_of_plant</BlastOutput_query-def>
+  <BlastOutput_query-len>630</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_expect>0.001</Parameters_expect>
+      <Parameters_sc-match>1</Parameters_sc-match>
+      <Parameters_sc-mismatch>-2</Parameters_sc-mismatch>
+      <Parameters_gap-open>0</Parameters_gap-open>
+      <Parameters_gap-extend>0</Parameters_gap-extend>
+      <Parameters_filter>L;m;</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+<BlastOutput_iterations>
+<Iteration>
+  <Iteration_iter-num>1</Iteration_iter-num>
+  <Iteration_query-ID>Query_1</Iteration_query-ID>
+  <Iteration_query-def>chunk_of_plant</Iteration_query-def>
+  <Iteration_query-len>630</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
+  <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def>
+  <Hit_accession>2</Hit_accession>
+  <Hit_len>23459830</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>1164.51</Hsp_bit-score>
+      <Hsp_score>630</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>630</Hsp_query-to>
+      <Hsp_hit-from>4341</Hsp_hit-from>
+      <Hsp_hit-to>4970</Hsp_hit-to>
+      <Hsp_query-frame>1</Hsp_query-frame>
+      <Hsp_hit-frame>1</Hsp_hit-frame>
+      <Hsp_identity>630</Hsp_identity>
+      <Hsp_positive>630</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>630</Hsp_align-len>
+      <Hsp_qseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_qseq>
+      <Hsp_hseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_hseq>
+      <Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>5</Statistics_db-num>
+      <Statistics_db-len>119146348</Statistics_db-len>
+      <Statistics_hsp-len>26</Statistics_hsp-len>
+      <Statistics_eff-space>71964315672</Statistics_eff-space>
+      <Statistics_kappa>0.46</Statistics_kappa>
+      <Statistics_lambda>1.28</Statistics_lambda>
+      <Statistics_entropy>0.85</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+</BlastOutput_iterations>
+</BlastOutput>
+
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py	Mon Dec 02 10:27:05 2013 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py	Tue Dec 03 10:02:17 2013 -0500
@@ -158,6 +158,11 @@
             # <Hit_accession>Subject_1</Hit_accession>
             #
             #apparently depending on the parse_deflines switch
+            #
+            #Or, with BLAST 2.2.28+ can get this,
+            # <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
+            # <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def>
+            # <Hit_accession>2</Hit_accession>
             sseqid = hit.findtext("Hit_id").split(None,1)[0]
             hit_def = sseqid + " " + hit.findtext("Hit_def")
             if re_default_subject_id.match(sseqid) \
@@ -165,6 +170,11 @@
                 #Place holder ID, take the first word of the subject definition
                 hit_def = hit.findtext("Hit_def")
                 sseqid = hit_def.split(None,1)[0]
+            if sseqid.startswith("gnl|BL_ORD_ID|") \
+            and sseqid == "gnl|BL_ORD_ID|" + hit.findtext("Hit_accession"):
+                #Alternative place holder ID, again take the first word of hit_def
+                hit_def = hit.findtext("Hit_def")
+                sseqid = hit_def.split(None,1)[0]
             # for every <Hsp> within <Hit>
             for hsp in hit.findall("Hit_hsps/Hsp"):
                 nident = hsp.findtext("Hsp_identity")
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Mon Dec 02 10:27:05 2013 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Tue Dec 03 10:02:17 2013 -0500
@@ -70,6 +70,16 @@
             <!-- Note this has some white space differences from the actual blastp output -->
             <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" />
         </test>
+        <test>
+            <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" />
+            <param name="out_format" value="std" />
+            <output name="tabular_file" file="blastn_arabidopsis.standard.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" />
+            <param name="out_format" value="ext" />
+            <output name="tabular_file" file="blastn_arabidopsis.extended.tabular" ftype="tabular" />
+        </test>
     </tests>
     <help>
     
@@ -122,7 +132,7 @@
     22 sseq          Aligned part of subject sequence
     23 qlen          Query sequence length
     24 slen          Subject sequence length
-    25 salltitles    All subject titles, separated by '&lt;&gt;'
+    25 salltitles    All subject title(s), separated by '&lt;&gt;'
 ====== ============= ===========================================
 
 Beware that the XML file (and thus the conversion) and the tabular output
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Mon Dec 02 10:27:05 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Dec 03 10:02:17 2013 -0500
@@ -13,7 +13,7 @@
     <xml name="input_out_format">
         <param name="out_format" type="select" label="Output format">
             <option value="6">Tabular (standard 12 columns)</option>
-            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 25 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -351,7 +351,7 @@
     22 sseq          Aligned part of subject sequence
     23 qlen          Query sequence length
     24 slen          Subject sequence length
-    25 salltitles    All subject titles, separated by '&lt;&gt;'
+    25 salltitles    All subject title(s), separated by '&lt;&gt;'
 ====== ============= ===========================================
 
 The third option is BLAST XML output, which is designed to be parsed by