NAME

Bio::SeqHash - get one or more sequences from a FASTA file quickly.

VERSION

version 0.1.4

SYNOPSIS

            

              
              
# use it in object-oriented way;
use Bio::SeqHash;
my $obj = Bio::SeqHash->new(file => "test.fa");
my $hs = $obj->fa2hs; # get a HashRef coverted from the test.fa
my $seq = $obj->get_seq("seq_id"); # get the sequence of "seq_id"(only the sequence)
my $seq_fa = $obj->get_id_seq("seq_id"); # get the sequence of "seq_id"(in the FASTA format)
$obj->get_seqs_batch('id_list.txt', 'output.fa');  # extract specified sequence to output file
# use it in Common mode;
use Bio::SeqHash "fa2hs";
my $hs = fa2hs("in.fa");
            
          

DESCRIPTION

Currently, there do have some modules that can operate the FASTA file such as Bio::SeqIO, But it only provide some basic operation to obtain the information about sequence. In my daily work, I still have to write some repetitive code. So this module is write to perform a deeper wrapper for operating FASTA file Notice: this module is not suitable for the FASTA file that is extremble big.

METHODS

fa2hs

            

              
              
Convert a fasta file into a HashRef variable. If the C<file> parameter have been passed
into during the process of new, here needs no parameter, otherwise you have to provide
the path of a fasta file.
            
          

get_id_seq

            

              
              
get a sequence by a id in FASTA format
            
          

get_seq

            

              
              
get a sequence by a id
            
          

get_seqs_batch

            

              
              
extract specified gene list from input file
            
          

AUTHOR

Yan Xueqing <yanxueqing621@163.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2017 by Yan Xueqing.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.