Mercurial > repos > erasmus-medical-center > hla_dq

changeset 1:4fc47a3ff9e8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit 3f631031b57350f0437e90e4de3352725bb84716
author erasmus-medical-center
date Wed, 30 May 2018 09:21:15 -0400
parents 10a407fb5072
children
files hla_dq.py hla_dq.xml test-data/test1_results.tsv test-data/test2_results.tsv
diffstat 4 files changed, 13 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/hla_dq.py	Wed May 30 07:50:21 2018 -0400
+++ b/hla_dq.py	Wed May 30 09:21:15 2018 -0400
@@ -42,12 +42,12 @@
 
     ''' each combination of DQA1,DQB1,type '''
     associated_combinations = [
-        ['02:01', '02:02', 'DQ2.2'],
-        ['03:03', '02:02', 'DQ2.3'],
-        ['05:01', '02:01', 'DQ2.5'],
-        ['03:01', '03:02', 'DQ8'],
-        ['03:02', '03:02', 'DQ8'],
-        ['03:03', '03:02', 'DQ8']]
+        ['02:01', '02:02', ' DQ2.2 (02:01-02:02)'],
+        ['03:03', '02:02', ' DQ2.3 (03:03-02:02)'],
+        ['05:01', '02:01', ' DQ2.5 (05:01-02:01)'],
+        ['03:01', '03:02', ' DQ8 (03:01-03:02)'],
+        ['03:02', '03:02', ' DQ8 (03:02-03:02)'],
+        ['03:03', '03:02', ' DQ8 (03:03-03:02)']]
 
     return [a[2] for a in associated_combinations
             if a[0] in typesA and a[1] in typesB]
@@ -83,4 +83,4 @@
             outfile.write(
                 'A' + str(bcount) + '\t' +
                 '\t'.join([';'.join(sorted(set(l)))
-                          if l else '-' for l in line])+'\n')
+                          if l else ' -' for l in line])+'\n')
--- a/hla_dq.xml	Wed May 30 07:50:21 2018 -0400
+++ b/hla_dq.xml	Wed May 30 09:21:15 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="hla_dq" name="HLA-DQ typing" version="1.0">
+<tool id="hla_dq" name="HLA-DQ typing" version="1.1">
     <description> Determine possible associated types given BLAST IMGT/HLA annotation</description>
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/hla_dq.py'
--- a/test-data/test1_results.tsv	Wed May 30 07:50:21 2018 -0400
+++ b/test-data/test1_results.tsv	Wed May 30 09:21:15 2018 -0400
@@ -1,3 +1,3 @@
 	B1	B2
-A1	-	-
-A2	-	DQ8
+A1	 -	 -
+A2	 -	 DQ8 (03:01-03:02)
--- a/test-data/test2_results.tsv	Wed May 30 07:50:21 2018 -0400
+++ b/test-data/test2_results.tsv	Wed May 30 09:21:15 2018 -0400
@@ -1,4 +1,4 @@
 	B1	B2	B3
-A1	-	-	DQ2.2
-A2	-	DQ8	DQ8
-A3	-	DQ8	DQ2.2;DQ2.3;DQ2.5;DQ8
+A1	 -	 -	 DQ2.2 (02:01-02:02)
+A2	 -	 DQ8 (03:01-03:02)	 DQ8 (03:01-03:02)
+A3	 -	 DQ8 (03:01-03:02); DQ8 (03:02-03:02); DQ8 (03:03-03:02)	 DQ2.2 (02:01-02:02); DQ2.3 (03:03-02:02); DQ2.5 (05:01-02:01); DQ8 (03:01-03:02); DQ8 (03:02-03:02); DQ8 (03:03-03:02)