Bio::I...::Fasta(3pm)

💖 Bio::Index::Fasta — bestie's guide to indexing fasta files 💖

okay so. you've got a bunch of fasta files. you've got vibes. and you want to find sequences in them without re-scanning the whole thing every single time like some kind of peasant? that's literally what this module is for. it's Bio::Index::Fasta, from the User Contributed Perl Documentation, and it's here to make your life ✨easy✨.

---

🌸 SYNOPSIS 🌸

first things first, bestie: make the index for one or more fasta files.

# Make an index for one or more fasta files
use Bio::Index::Fasta;
use strict;

my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name,
                                 -write_flag => 1);
$inx->make_index(@ARGV);

and then — plot twist — once the index is built, you can access it. same script, different script, whatever, it does not care:

# Once the index is made it can accessed, either in the
# same script or a different one
use Bio::Index::Fasta;
use strict;

my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name);
my $out = Bio::SeqIO->new(-format => 'Fasta',
                          -fh => \*STDOUT);

foreach my $id (@ARGV) {
    my $seq = $inx->fetch($id); # Returns Bio::Seq object
     $out->write_seq($seq);
}

# or, alternatively
my $id;
my $seq = $inx->get_Seq_by_id($id); # identical to fetch()

not me showing you two whole ways to grab a sequence. fetch() and get_Seq_by_id() are literally the same thing. pick your fighter. 🫶

---

🦋 DESCRIPTION 🦋

so this module inherits all the dbm-file-managing functions from Bio::Index::Abstract.pm, and then it handles the basic functionality for indexing fasta files and pulling the sequence back out of them. for best results, use strict. no cap, just do it.

Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, which means it can be used as a Sequence database for other parts of bioperl. it's giving team player. 💅

there's more example code hanging out in scripts/index/ if you want to peek.

heads up! by default, the key for the sequence is the first continuous string after the > in the fasta header. if you want a specific substring of the fasta header instead, you must use the id_parser() method. don't skip that step, bestie, it matters.

you can also set or customize the unique key used to retrieve stuff by writing your own function and calling the id_parser() method. for example:

$inx->id_parser(\&get_id);
# make the index
$inx->make_index($file_name);

# here is where the retrieval key is specified
sub get_id {
   my $line = shift;
   $line =~ /^>.+gi\|(\d+)/;
   $1;
}

---

🌈 FEED_BACK 🌈

💌 Mailing Lists 💌

user feedback is an integral part of the evolution of this and other Bioperl modules. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated. 💖

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫶 Support 🫶

please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. many experienced and reponsive experts will be able look at the problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible. the more context you give, the faster someone can help you. iconic behavior. ✨

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

---

👑 AUTHOR - James Gilbert 👑

Email - jgrg@sanger.ac.uk

---

🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _. (iykyk — underscore means "not your business, bestie, that's internal.")

🔧 _file_format 🔧

Title   : _file_format
Function: The file format for this package, which is needed
          by the SeqIO system when reading the sequence.
Returns : 'Fasta'

🔧 _index_file 🔧

Title   : _index_file
Usage   : $index->_index_file( $file_name, $i )
Function: Specialist function to index FASTA format files.
          Is provided with a filename and an integer
          by make_index in its SUPER class.
Example :
Returns :
Args    :

🔧 id_parser 🔧

Title   : id_parser
Usage   : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
          parse the ID for record from a string.  Useful
          for (for instance) specifying a different
          parser for different flavours of FASTA file.
          Returns \&default_id_parser (see below) if not
          set. If you supply your own id_parser
          subroutine, then it should expect a fasta
          description line.  An entry will be added to
          the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : ref to CODE if called without arguments
Args    : CODE

🔧 default_id_parser 🔧

Title   : default_id_parser
Usage   : $id = default_id_parser( $header )
Function: The default Fasta ID parser for Fasta.pm
          Returns $1 from applying the regexp /^>\s*(\S+)/
          to $header.
Returns : ID string
Args    : a fasta header line string

---

and that's the whole page, bestie! 💖✨🌸 this one's perl v5.32.1, dated 2021-08-15, straight from the User Contributed Perl Documentation for Bio::I...::Fasta(3pm). go index something iconic. periodt. 💅🦋