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.
Faidx -- Perl extension for accessing bgzip compressed and indexed FASTA using
htslib
#include the module
use Bio::DB::HTS::Faidx;
#create the index object
my $fasta = "$Bin/data/Saccharomyces_cerevisiae.R64-1-1.dna.chromosome.I.fa.gz" ;
my $location = "I:1-100" ;
my $seq_id = "I" ;
my $index = Bio::DB::HTS::Faidx->new($fasta);
#get sequence using the location
my $seq = "" ;
my $length = 0 ;
($seq, $length) = $index->get_sequence($location);
$seq = $index->get_sequence_no_length($location);
$length = $index->length($seq_id);
#get sequence using the separate parameters.
#Note here that the sequence start and end points are zero indexed, so code accordingly.
($seq, $length) = $index->get_sequence2("I",1,99);
$seq = $index->get_sequence2_no_length("I",1,99);
my @seq_ids = $index->get_all_sequence_ids();
#returns 1 if sequence ID is present, 0 if not
my $has_seq = $index->has_sequence('I');
Rishi Nag