Mercurial > repos > ebi-gxa > gtf2gene_list
comparison gtf2featureAnnotation.R @ 5:00ee933b08fd draft
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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| 4:b6354c917ef9 | 5:00ee933b08fd |
|---|---|
| 152 } | 152 } |
| 153 | 153 |
| 154 # Version transcripts | 154 # Version transcripts |
| 155 | 155 |
| 156 if ( opt$feature_type == 'transcript' && opt$version_transcripts && all(c('transcript_id', 'transcript_version') %in% colnames(anno) )){ | 156 if ( opt$feature_type == 'transcript' && opt$version_transcripts && all(c('transcript_id', 'transcript_version') %in% colnames(anno) )){ |
| 157 anno$transcript_id <- paste(anno$transcript_id, anno$transcript_version, sep='.') | 157 has_transcript_version <- ! is.na(anno$transcript_version) |
| 158 anno$transcript_id[has_transcript_version] <- paste(anno$transcript_id[has_transcript_version], anno$transcript_version[has_transcript_version], sep='.') | |
| 158 } | 159 } |
| 159 | 160 |
| 160 # If specified, filter down a provided cDNA FASTA file | 161 # If specified, filter down a provided cDNA FASTA file |
| 161 | 162 |
| 162 if (! is.null(opt$filter_cdnas)){ | 163 if (! is.null(opt$filter_cdnas)){ |