focal (3) Bio::DB::HTS::Kseq.3pm.gz

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