GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
Bio::Phylo::Parsers::Fastq(3) User Contributed Perl Documentation Bio::Phylo::Parsers::Fastq(3)
 

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.
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>

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>
2017-10-30 perl v5.28.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.