[Gmod-schema-cmts] schema/GMODTools/bin gff2biomart5.pl,NONE,1.1

[Don G. <don...@us...>]

Update of /cvsroot/gmod/schema/GMODTools/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19108/bin

Added Files:
	gff2biomart5.pl 
Log Message:
biomart build script;  prerel. updates

--- NEW FILE: gff2biomart5.pl ---
#!/usr/bin/perl

=head1 NAME

  gff2biomart.pl -- create tables for BioMart from genome GFF annotations

=head1 SYNOPSIS

./gff2biomart.pl --species=scer --version=sgdlite_2005_08_23 --output tabscer/ \
 --fasta $scer/fasta/*-all-chromosome-*.fasta  \
 $scer/gff/scer-chr*.gff

  # add some extra tables here for more filters
./gff2biomart3.pl -dataset=11 -species=dper -version=br051028 -output tabdper \
 -table=cross_genome_match_dmelchr,match_tblastn_modDM \
 -fasta $dper/dper*.fa.gz $dper/gff/dper*scaffold*gff $dper/gff/dper*gff.gz

Example data sets from this tool are at:
http://insects.eugenes.org/BioMart/martview
[...1528 lines suppressed...]
<AttributeDescription displayName="end" internalName="end" />
<AttributeDescription displayName="strand" internalName="strand" />
<AttributeDescription displayName="rank" internalName="rank" />
<AttributeDescription internalName="seq_edits" />
<AttributeDescription internalName="type" />
</AttributeCollection>
</AttributeGroup>
</AttributePage>

</DatasetConfig>
EOF

}




1; # turn into perl module
##=================================