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Manual Reference Pages  -  BIO::PHYLO::PARSERS::FASTQ (3)

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NAME

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

CONTENTS

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, # dont 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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::PARSERS::FASTQ (3) 2014-02-08

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