Mercurial > repos > ebi-gxa > gtf2gene_list

diff gtf2featureAnnotation.R @ 5:00ee933b08fd draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 2d7ec5b8aa6d292cbb4a1b60efd1d98ff23263ba
author ebi-gxa
date Fri, 01 Nov 2019 09:44:26 -0400
parents 247b439a78f7
children
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--- a/gtf2featureAnnotation.R	Fri Oct 25 09:25:20 2019 -0400
+++ b/gtf2featureAnnotation.R	Fri Nov 01 09:44:26 2019 -0400
@@ -154,7 +154,8 @@
 # Version transcripts
 
 if ( opt$feature_type == 'transcript' && opt$version_transcripts && all(c('transcript_id', 'transcript_version') %in% colnames(anno) )){
-  anno$transcript_id <- paste(anno$transcript_id, anno$transcript_version, sep='.')
+  has_transcript_version <- ! is.na(anno$transcript_version)
+  anno$transcript_id[has_transcript_version] <- paste(anno$transcript_id[has_transcript_version], anno$transcript_version[has_transcript_version], sep='.')
 }
 
 # If specified, filter down a provided cDNA FASTA file