Creation of ${GTF_FILE_BASE}.gene.bed and ${GTF_FILE_BASE}.exon.bed needs to operate off column matching

[bryce-turner]

jetstream_resources/shared_resource_creation_scripts/create_gene_model.sh

Lines 247 to 258 in 6ffe268

	# Create a bed file for the start and stop for each gene
	awk -F '[\t"]' '$1 !~ /^#/ { if (a[$10] == "" ) { a[$10] = $1 ; b[$10] = $4 ; c[$10] = $5 ; next } ;
	if ($4 < b[$10]) { b[$10] = $4 } ;
	if ($5 > c[$10]) { c[$10] = $5 }
	} END {
	for (i in a) {
	OFS = "\t" ; print a[i], b[i], c[i], i
	}
	}' ${GTF_FILE} | sort -k1,1V -k2,2n -k3,3n > ${GTF_FILE_BASE}.gene.bed
	# Create a bed file for the start and stop of each exon for each gene
	awk -F '[\t"]' '$1 !~ /^#/ { if ($3 == "exon") { OFS = "\t" ; print $1, $4, $5, $10 }}' ${GTF_FILE} | sort -k1,1V -k2,2n -k3,3n > ${GTF_FILE_BASE}.exon.bed

We grab the value in column 10, e.g. $10, but this value is not always the gene_id value. For example we have the following for canfam3.1 ensemble 98:

X	ensembl	gene	21422	25435	.	+	.	gene_source "ensembl"; gene_biotype "lncRNA"; transcript_id "ENSCAFG00000039510"; transcript_name "ENSCAFG00000039510"; gene_version "2"; gene_name "ENSCAFG00000039510"; gene_id "ENSCAFG00000039510"

Instead we might be able to grab the column for gene_id and add 1. For example:

awk -F '[\t"]' '$1 !~ /^#/ { for (i=1; i<=NF; i++) { f[$i] = i } if (a[$(f["gene_id"]+1)] == "" ) { a[$(f["gene_id"]+1)] = $1 ; b[$(f["gene_id"]+1)] = $4 ; c[$(f["gene_id"]+1)] = $5 ; next } ;
        if ($4 < b[$(f["gene_id"]+1)]) { b[$(f["gene_id"]+1)] = $4 } ;
        if ($5 > c[$(f["gene_id"]+1)]) { c[$(f["gene_id"]+1)] = $5 }
} END {
for (i in a) {
        OFS = "\t" ; print a[i], b[i], c[i], i
}
}' ${GTF_FILE} | sort -k1,1V -k2,2n -k3,3n > ${GTF_FILE_BASE}.gene.bed

[PedalheadPHX]

This should really be based on a program that can read a GTF, maybe look if we can adopt the container we were working to sort out, it has lots of functions to parse gff and gtf files that might simplify this, otherwise you are correct we need to discover the position