John A. Crow > Bio-SeqReader > Bio::SeqReader::Fasta

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Bio-SeqReader-0.1.3.tar.gz

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NAME ^

Bio::SeqReader::Fasta - Class providing a reader for files in FASTA format.

SYNOPSIS ^

  use Bio::SeqReader::Fasta;
  my $in1 = new Bio::SeqReader::Fasta();             # from stdin
  my $fh = ...
  my $in2 = new Bio::SeqReader::Fasta( fh => $fh );  # from filehandle

DESCRIPTION ^

Bio::SeqReader::Fasta provides a method for reading a file or stream in FASTA format.

CLASS METHODS ^

Bio::SeqReader::Fasta provides no class methods.

INSTANCE METHODS ^

Bio::SeqReader::Fasta provides the following instance methods.

new()

Returns a new Bio::SeqReader::Fasta object associated with stdin or with a filehandle.

  # From an IO::File filehandle
  my $fh1 = new IO::File( 'in.fq' );
  my $in1 = new Bio::SeqReader::Fasta( fh => $fh1);

  # From an IO::Uncompress::AnyUncompress filehandle
  my $fh2 = new IO::File( 'in.fq.gz' );
  my $in2 = new Bio::SeqReader::Fasta( fh => $fh2);

  # From stdin
  my $in3 = new Bio::SeqReader::Fasta();

A specified filehandle must be compatible with those produced by IO::File filehandle; for example,

  $fh1 = new IO::File( 'in.fasta' )
  $fh2 = new IO::Uncompress::AnyUncompress( 'in.fasta.gz' )
  $fh3 = new IO::Uncompress::AnyUncompress( 'in.fasta' ).
next()

Returns the next sequence as a Bio::SeqReader::FastaRecord object.

  while ( my $so = $in->next() ) {
      ... work with $so here ...
  }

EXTERNAL DEPENDENCIES ^

Perl core.

EXAMPLES ^

  # Open and read a file in FASTA format
  my $fh = new IO::File( 'foo.fasta' );
  my $in = new Bio::SeqReader( fh => $fh );
  while ( my $so = $in->next() ) {
      my $s = $so->seq();   # $so is a Bio::SeqReader::FastaRecord
      . . .
  }

  # Open and read a gzipped file in FASTA format
  my $fh = new IO::Uncompress::AnyUncompress( 'foo.fasta.gz' );
  my $in = new Bio::SeqReader( fh => $fh );
  while ( my $so = $in->next() ) {
      my $s = $so->seq();   # $so is a Bio::SeqReader::FastaRecord
      . . .
  }

BUGS ^

None reported yet, but let me know.

SEE ALSO ^

Bio::SeqReader::FastaRecord, Bio::SeqReader.

AUTHOR ^

John A. Crow <jac_at_cpan_dot_org>

COPYRIGHT AND LICENSE ^

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.

  Copyright (C) 2012 by John A. Crow
  Copyright (C) 2012 by National Center for Genome Resources
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