Robert Buels > Bio-GFF3 > Bio::GFF3::Transform::FromFasta

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Bio-GFF3-2.0.tar.gz

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Module Version: 2.0   Source  

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_fhs

Arrayref 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.

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