update ensembl hg19

Author: stevekm

Makefile

@@ -5,12 +5,12 @@
 none:
 
 # make all sets of annotations
-all: gencode ensembl gencode-hg38 ensembl-hg38
+all: gencode-hg19 ensembl-hg19 gencode-hg38 ensembl-hg38
 
 
 # ~~~~~ GENCODE hg19 ~~~~~ #
 # generate the Gencode hg19 annotations .bed file
-gencode: gencode.v19.annotation.genes.bed
+gencode-hg19: gencode.v19.annotation.genes.bed
 
 gencode.v19.annotation.gtf.gz: 
 	wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
@@ -36,27 +36,20 @@ gencode.v27.annotation.genes.bed: gencode.v27.annotation.gtf.gz
 
 # ~~~~~ ENSEMBL hg19 ~~~~~ #
 # generate the Ensembl hg19 annotations .bed file
-ensembl: Homo_sapiens.GRCh37.82.noGLMT.chr.genes.bed
+ensembl-hg19: Homo_sapiens.GRCh37.82.chr.bed
 
-Homo_sapiens.GRCh37.82.gtf.gz: 
-	wget ftp://ftp.ensembl.org/pub/grch37/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh37.82.gtf.gz
+Homo_sapiens.GRCh37.82.chr.gtf.gz: 
+	wget ftp://ftp.ensembl.org/pub/grch37/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh37.82.chr.gtf.gz
 
-# Need to filter out the GL, MT entries
-Homo_sapiens.GRCh37.82.noGLMT.gtf: Homo_sapiens.GRCh37.82.gtf.gz
-	zcat Homo_sapiens.GRCh37.82.gtf.gz | grep -Ev "^#|^GL|^M" > Homo_sapiens.GRCh37.82.noGLMT.gtf
-
-# need to add 'chr' to the start of each 1st entry
-Homo_sapiens.GRCh37.82.noGLMT.chr.gtf: Homo_sapiens.GRCh37.82.noGLMT.gtf
-	cat Homo_sapiens.GRCh37.82.noGLMT.gtf | sed 's/^/chr/' > Homo_sapiens.GRCh37.82.noGLMT.chr.gtf
+# remove comment lines
+# extract only 'gene' entries
+# add 'chr' to first entry, change 'chrMT' to 'chrM'
+Homo_sapiens.GRCh37.82.chr.gtf: Homo_sapiens.GRCh37.82.chr.gtf.gz
+	zcat Homo_sapiens.GRCh37.82.chr.gtf.gz | grep -Ev '^#' | grep -w 'gene' | sed -e 's/^/chr/' -e 's/^chrMT/chrM/' > Homo_sapiens.GRCh37.82.chr.gtf
 
 # convert to .bed
-Homo_sapiens.GRCh37.82.noGLMT.chr.bed: Homo_sapiens.GRCh37.82.noGLMT.chr.gtf
-	gtf2bed < Homo_sapiens.GRCh37.82.noGLMT.chr.gtf > Homo_sapiens.GRCh37.82.noGLMT.chr.bed
-
-# extract genes
-Homo_sapiens.GRCh37.82.noGLMT.chr.genes.bed: Homo_sapiens.GRCh37.82.noGLMT.chr.bed
-	grep -w gene Homo_sapiens.GRCh37.82.noGLMT.chr.bed > Homo_sapiens.GRCh37.82.noGLMT.chr.genes.bed
-
+Homo_sapiens.GRCh37.82.chr.bed: Homo_sapiens.GRCh37.82.chr.gtf
+	gtf2bed < Homo_sapiens.GRCh37.82.chr.gtf > Homo_sapiens.GRCh37.82.chr.bed
 
 
 
@@ -86,6 +79,8 @@ Homo_sapiens.GRCh38.91.chr.bed: Homo_sapiens.GRCh38.91.chr.gtf
 	Homo_sapiens.GRCh37.82.noGLMT.chr.gtf \
 	gencode.v27.annotation.gtf.gz \
 	Homo_sapiens.GRCh38.91.chr.gtf \
-	Homo_sapiens.GRCh38.91.chr.gtf.gz
+	Homo_sapiens.GRCh38.91.chr.gtf.gz \
+	Homo_sapiens.GRCh37.82.chr.gtf \
+	Homo_sapiens.GRCh37.82.chr.gtf.gz