Bio::DB::HTS::Kseq

LICENSE

Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

NAME

Bio::DB::HTS::Kseq - Bindings to Kseq

DESCRIPTION

Bindings to the Kseq library for iterating through a locally held FASTA/FASTQ file very quickly. Supports compressed and uncompressed files alongside filehandles.

SYNOPSIS

  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