# 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 <[email protected]>

# 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.

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