# 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 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 # 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.