NAME

Faidx - Perl extension for accessing bgzip compressed and indexed FASTA using htslib

SYNOPSIS

#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');

AUTHOR

Rishi Nag

COPYRIGHT AND LICENSE

# Copyright [1999-2016] Wellcome Trust Sanger Institute and the 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.