Copyright [2015-2017] 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.
Bio::DB::HTS::Kseq - Bindings to Kseq
Bindings to the Kseq library for iterating through a locally held FASTA/FASTQ file very quickly. Supports compressed and uncompressed files alongside filehandles.
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
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
To install Bio::DB::HTS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DB::HTS
CPAN shell
perl -MCPAN -e shell install Bio::DB::HTS
For more information on module installation, please visit the detailed CPAN module installation guide.