sgd_to_gff.pl - Massage SGD's feature dump format into a form suitable for Bio::DB::GFF
perl sgd_to_gff.pl chromosomal_features.tab > sgd.gff
This script massages the SGD yeast sequence feature file located at ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_feature.tab into a GFF format suitable for use with Bio::DB::GFF. This lets you view the yeast annotations with the generic genome browser (http://www.gmod.org).
To use this script, get the SGD features file at the above URL. Then run this command:
sgd_to_gff.pl chromosomal_feature.tab > sgd.gff
The resulting database will have the following feature types (represented as "method:source"):
Component:chromosome A chromosome gene:sgd A named gene rRNA:sgd A ribosomal RNA ARS:sgd An origin of replication CEN:sgd Centromere snRNA:sgd Small nuclear RNA RNA:sgd An RNA gene ORF:sgd An open reading frame ORF|Pseudogene:sgd A probably pseudogene LTR:sgd A long terminal repeat Ty ORF:sgd ?? Transposon:sgd A transposon Pseudogene|Ty ORF:sgd ?? snoRNA:sgd Small nucleolar RNA tRNA:sgd Transfer RNA
Lincoln Stein <lstein@cshl.org>
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.