Bio::DB::HTS::Kseq3pm
Bindings to kseq
Usage
my $kseq = Bio::DB::HTS::Kseq->new('path/to/file');my $iter = $kseq->iterator();while(my $r = $iter->next_seq()) {say $r->name;say $r->desc;say $r->seq;say $r->qual;}# Allowing the object to go out of scope will close down all file handles
Methods
- "new"
-
my $kseq = Bio::DB::HTS::Kseq->new('path/to/file');Returns an instance of this object from a file path.
- "newfh"
-
open my $fh, '<', 'path' or die "Cannot open path: $!";binmode $fh;my $kseq = Bio::DB::HTS::Kseq->newfh($fh);Returns an instance of this object from an opened file handle. This supports any known Perl glob/filehandle type
- "iterator"
-
my $iter = $kseq->iterator();Returns the kseq iterator object
Overview
Bindings to the Kseq library for iterating through a locally held FASTA/FASTQ file very quickly. Supports compressed and uncompressed files alongside filehandles.
Releases
3 releases since Debian 11 (Bullseye); the text changed 2 times.