Bio::GFF3::Transform::FromFasta - make gff3 for the sequences in a fasta file
use Bio::GFF3::Transform::FromFasta 'gff3_from_fasta'; gff3_from_fasta( in => [ 'file1', $filehandle, ... ], out => \*STDOUT, type => 'contig', fasta_section => 1, source => 'MyAnalysis', );
in => \@files_or_fhs
Arrayref of filenames or filehandles containing FASTA.
out => $file,
Filename or filehandle to write GFF3 to.
type => 'SO_type',
String Sequence Ontology term name for the features being made.
source => 'fasta',
Source name to put in the gff3. Default 'fasta'.
fasta_section => 0,
Default off. if true, write the actual sequencesh '##FASTA' section.
Robert Buels <rmb32@cornell.edu>
This software is copyright (c) 2012 by Robert Buels.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
To install Bio::GFF3::LowLevel, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::GFF3::LowLevel
CPAN shell
perl -MCPAN -e shell install Bio::GFF3::LowLevel
For more information on module installation, please visit the detailed CPAN module installation guide.