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