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# Ensembl GTF file distributed by Ensembl for hg38
# Cleans GTF file by converting chromosome names to standard names
# Uses https://github.com/dpryan79/ChromosomeMappings to remap the chromosome names
---
attributes:
name: gtf
version: 78
recipe:
full:
recipe_type: bash
recipe_cmds:
- |
url=http://ftp.ensembl.org/pub/release-78/gtf/homo_sapiens/Homo_sapiens.GRCh38.78.gtf.gz
mkdir -p rnaseq
remap_url=http://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_ensembl2UCSC.txt
wget --no-check-certificate -qO- $remap_url | awk '{if($1!=$2) print "s/^"$1"/"$2"/g"}' > remap.sed
wget --no-check-certificate -qO- $url | gunzip | sed -f remap.sed | grep -v "*_*_alt" > rnaseq/hg38.gtf
rm remap.sed
recipe_outfiles:
- rnaseq/hg38.gtf
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