Bio::Polloc::LocusIO - I/O interface of Bio::Polloc::Locus::* objects
Bio::Polloc::Locus::*
Email lmrodriguezr at gmail dot com
Bio::Polloc::Polloc::Root
Bio::Polloc::Polloc::IO
Read & write loci:
use strict; use Bio::Polloc::LocusIO; my $locusI = Bio::Polloc::LocusIO->new(-file=>"t/loci.gff3", -format=>"gff3"); my $locusO = Bio::Polloc::LocusIO->new(-file=>">out.gff3", -format=>"gff3"); while(my $locus = $locusI->next_locus){ print "Got a ", $locus->type, " from ", $locus->from, " to ", $locus->to, "\n"; # Filter per type if($locus->type eq "repeat"){ $locusO->write_locus($locus); } }
Methods provided by the package
The basic initialization method
Gets/sets the format of the file
Format (str), currently supported: gff3.
Format (str or undef).
undef
Appends one locus to the output file.
The locus to append.
If true, forces re-parsing of the locus. Otherwise, tries to load cached parsing (if any).
Gets the loci stored in the input file.
An arrayref containing the Bio::Polloc::Genome objects associated to the collection of loci. This is not mandatory, but seq and genome properties will not be set on the newly created objects if this parameter is not provided.
seq
genome
A Bio::Polloc::LociGroup object.
Reads the next locus in the buffer.
Same of read_loci
A Bio::Polloc::LocusI object.
Methods intended to be used only within the scope of Bio::Polloc::*
Uniformizes the distinct names that every format can receive
The requested format (str)
The qualified format (str or undef)
Format-specific implementation of write_locus.
write_locus
Format-specific implementation of next_locus.
next_locus
To install Bio::Polloc, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Polloc
CPAN shell
perl -MCPAN -e shell install Bio::Polloc
For more information on module installation, please visit the detailed CPAN module installation guide.