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Top Forums Shell Programming and Scripting Getting unique sequences from multiple fasta file Post 303022717 by vgersh99 on Wednesday 5th of September 2018 04:25:20 PM
Old 09-05-2018
Code:
awk '{ a[$0]} END{for (i in a) print i ORS}' RS= my_file.fasta

or better yet:
Code:
awk '!a[$0]++' RS= ORS='\n\n' my_file.fasta


Last edited by vgersh99; 09-06-2018 at 10:57 AM..
These 2 Users Gave Thanks to vgersh99 For This Post:
 

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Bio::Index::Fasta(3pm)					User Contributed Perl Documentation				    Bio::Index::Fasta(3pm)

NAME
Bio::Index::Fasta - Interface for indexing (multiple) fasta files SYNOPSIS
# 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); # 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() DESCRIPTION
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing fasta files, and retrieving the sequence from them. For best results 'use strict'. Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning it can be used as a Sequence database for other parts of bioperl Additional example code is available in scripts/index/*PLS and in the Bioperl Tutorial (<http://www.bioperl.org/wiki/Bptutorial.pl>) Note that by default the key for the sequence will be the first continuous string after the '>' in the fasta header. If you want to use a specific substring of the fasta header you must use the id_parser() method. You can also set or customize the unique key used to retrieve 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. 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://redmine.open-bio.org/projects/bioperl/ 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 _ _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 perl v5.14.2 2012-03-02 Bio::Index::Fasta(3pm)
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