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Man Pages


Manual Reference Pages  -  BIO::GFF3::TRANSFORM::FROMFASTA (3)

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NAME

Bio::GFF3::Transform::FromFasta - make gff3 for the sequences in a fasta file

CONTENTS

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 => CW$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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perl v5.20.3 BIO::GFF3::TRANSFORM::FROMFASTA (3) 2014-02-28

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