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| Bio::GFF3::Transform::FromFasta(3) | User Contributed Perl Documentation | Bio::GFF3::Transform::FromFasta(3) |
NAME
Bio::GFF3::Transform::FromFasta - make gff3 for the sequences in a fasta file
SYNOPSIS
use Bio::GFF3::Transform::FromFasta 'gff3_from_fasta';
gff3_from_fasta(
in => [ 'file1', $filehandle, ... ],
out => \*STDOUT,
type => 'contig',
fasta_section => 1,
source => 'MyAnalysis',
);
FUNCTIONS
gff3_from_fasta( in => \@files_or_fhs, out => $fh, type => 'SO_type' )
Arguments
- in
-
in => \@files_or_fhsArrayref of filenames or filehandles containing FASTA.
- out
-
out => $file,Filename or filehandle to write GFF3 to.
- type
-
type => 'SO_type',String Sequence Ontology term name for the features being made.
- source
-
source => 'fasta',Source name to put in the gff3. Default 'fasta'.
- fasta_section
-
fasta_section => 0,Default off. if true, write the actual sequencesh '##FASTA' section.
AUTHOR
Robert Buels <rmb32@cornell.edu>
COPYRIGHT AND LICENSE
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.
| 2014-02-28 | perl v5.40.2 |
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