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NAMEBio::Phylo::Parsers::Fastq - Parser used by Bio::Phylo::IO, no serviceable parts inside DESCRIPTIONA 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 ALSOThere is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.
CITATIONIf 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>
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