Bio::Phylo::Parsers::Fastq - Parser used by Bio::Phylo::IO, no serviceable parts inside
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"; } } );
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The fasta parser is called by the Bio::Phylo::IO object. Look there to learn more about parsing.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com
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
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.