Calculate transcript length of GTF file

gtf_transcript_length

# resource: http://seqanswers.com/forums/showthread.php?t=4914
# Calculate length for each transcript for a GTF file
awk -F"\t" '
$3=="exon" 
    {
        ID=substr($9, length($9)-16, 15); 
        L[ID]+=$5-$4+1
    } 
END{
    for(i in L)
        {print i"\t"L[i]}
    }
' gtf-file >output


#gtf-file
#chr1	hg19_ensGene	exon	66999066	66999090	0.000000	+	.	gene_id "ENSG00000118473"; gene_name "SGIP1"; transcript_id "ENST00000237247";
#chr1	hg19_ensGene	start_codon	67000042	67000044	0.000000	+	.	gene_id "ENSG00000118473"; gene_name "SGIP1"; transcript_id "ENST00000237247";
#chr1	hg19_ensGene	CDS	67000042	67000051	0.000000	+	0	gene_id "ENSG00000118473"; gene_name "SGIP1"; transcript_id "ENST00000237247";

#output
#ENST00000397500 2194
#ENST00000344941 2923
#ENST00000397501 4715

Modification suggested:

awk -F"\t" '
$3=="Exon" {
match($9, /ENSMUST[0-9]+.[0-9]+/);
if (RSTART) {
ID = substr($9, RSTART, RLENGTH);
L[ID] += $5 - $4 + 1;
}
}
END {
for(i in L) {
print i"\t"L[i]
}
}
' gtf-file > output