NAME

Bio::Phylo::Parsers::Fastq - Parser used by Bio::Phylo::IO, no serviceable parts inside

DESCRIPTION

A FASTQ file parser. To use it, you need to pass an argument that specifies the data type of the phred scores into the parse function, i.e.

 my $handler_type = _DATUM_;
 parse(
    -format => 'fastq',
    -type   => 'illumina', # to indicate how phred scores are scaled
    -file   => 'infile.fastq',
    -flush  => 1, # don't store record, flush and move on
    -handlers => {
    
        # specifies a handler that is executed on each newly created datum
        $handler_type => sub {
            my $seq = shift;
            my @char = $seq->get_char;
            my @anno = @{ $seq->get_annotations };
            
            # print fasta, omit bases with low phred scores
            print ">$seq\n";
            for my $i ( 0 .. $#char ) {
                if ( $anno[$i]->{phred} > 20 ) {
                    print $char[$i];
                }
            }
            print "\n";
        }
    }
 );

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Bio::Phylo::IO

The fasta parser is called by the Bio::Phylo::IO object. Look there to learn more about parsing.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63