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