Hello
I have the maize reference annotation downloaded from http://ftp.maizesequence.org/current/working-set/
the first 10 lines are as under:
How can I output transcript/feature length from the given genome coordinates? Is there a simple perl script out there? Or is there some script available in ENSembL API? Any help or suggestions appreciated?
thanks
Siva
I have the maize reference annotation downloaded from http://ftp.maizesequence.org/current/working-set/
the first 10 lines are as under:
Code:
UNKNOWN ensembl chromosome 1 14680007 . . . ID=UNKNOWN;Name=chromosome:AGPv1:UNKNOWN:1:14680007:1 UNKNOWN ensembl CDS 17354 17446 . + 0 Parent=GRMZM2G524142_T01;Name=CDS.1254885 UNKNOWN ensembl exon 17354 17460 . + . Parent=GRMZM2G524142_T01;Name=GRMZM2G524142_E01 UNKNOWN ensembl gene 17354 17460 . + . ID=GRMZM2G524142;Name=GRMZM2G524142;biotype=protein_coding UNKNOWN ensembl mRNA 17354 17460 . + . ID=GRMZM2G524142_T01;Parent=GRMZM2G524142;Name=GRMZM2G524142_T01;biotype=protein_coding UNKNOWN ensembl exon 17537 17976 . - . Parent=GRMZM2G369735_T01;Name=GRMZM2G369735_E03 UNKNOWN ensembl gene 17537 18259 . - . ID=GRMZM2G369735;Name=GRMZM2G369735;biotype=protein_coding UNKNOWN ensembl mRNA 17537 18259 . - . ID=GRMZM2G369735_T01;Parent=GRMZM2G369735;Name=GRMZM2G369735_T01;biotype=protein_coding UNKNOWN ensembl CDS 17716 17952 . - . Parent=GRMZM2G369735_T01;Name=CDS.1254890 UNKNOWN ensembl exon 17972 18045 . - . Parent=GRMZM2G369735_T02;Name=GRMZM2G369735_E02
thanks
Siva
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