add gene name to bed file

[cmccabe]

I am trying to add the gene_name to a bed file and I think the method I used below is using the gene_id instead. Is it possible to get the gene_name and maybe exon_number? Thank you .

$ wget ftp://ftp.sanger.ac.uk/pub/gencode/release_21/gencode.21.annotation.gtf.gz
$ gunzip --stdout gencode.v21.annotation.gtf.gz \
    | gtf2bed - \
    | grep "exon" \
    > gencode.exons.bed

followed by:

bedmap --echo --echo-map-id-uniq epilepsy70_medex_edit.bed gencode.exons.bed > answer.bed

The files are too large too attach, but here are a few lines:

gencode.exons.bed

chr1	11868	12227	ENSG00000223972.5	.	+	HAVANA	exon	.	gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1	12009	12057	ENSG00000223972.5	.	+	HAVANA	exon	.	gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1	12178	12227	ENSG00000223972.5	.	+	HAVANA	exon	.	gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1	12612	12697	ENSG00000223972.5	.	+	HAVANA	exon	.	gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 3; exon_id "ENSE00001758273.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; transcript_support_level "NA"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";

answer.bed (as of now)

chr1	43408884	43409004
|
chr1	43424253	43424373
|ENSG00000198198.11
chr1	154540492	154540612
|
chr1	154541927	154542093
|ENSG00000163239.10

epilepsy70_medex_edit.bed

chr1	40539722	40539865
chr1	40542489	40542609
chr1	40544221	40544341
chr1	40546054	40546174
chr1	40555071	40555194

Thank you .