Getting unique sequences from multiple fasta file Post: 303022716

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Top Forums Shell Programming and Scripting Getting unique sequences from multiple fasta file Post 303022716 by Ibk on Wednesday 5th of September 2018 04:13:49 PM

09-05-2018

Registered User

Getting unique sequences from multiple fasta file

Hi,

I have a fasta file with multiple sequences. How can i get only unique sequences from the file.

For example
my_file.fasta

Code:

>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC

>seq2
CAATTTTGGCTCCTTCATGTCTGTTGTGCCAGACTTGAGTGAGTTTGAACTGCAAGCAAGAAAGGCAGGTTCAGACCAAGAAAAAGATGCAATATACTCCAAGGCACTGATAGCAGCCACAAGAAAGGCGGCTCCTATTG

>seq3
CGGCCTGTGCATGGACATCAAGCAACGACATGGTGACAAAAGGGCTCAAGTGGTTCGAGGATCAGATAACAAAAGAGAATCCTAAATTTATCTCTTGGCACAAGGAGTATGAATTTTTCAAAAAGAATGTGCCCACAGTT

>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC

>seq4
AAACTGCAACTCTCACAAGCAAAGTTGTGGCACAGTTCTCAGTTCCTGGGGTCTATGTTGTTGCTGTGCAAGATATGATCAAAGACATGGTTGCCAGAAGAGGTGGAGGGCCTAAACGCGGAGTCAGTGATGAACACATC

>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC

>seq2
CAATTTTGGCTCCTTCATGTCTGTTGTGCCAGACTTGAGTGAGTTTGAACTGCAAGCAAGAAAGGCAGGTTCAGACCAAGAAAAAGATGCAATATACTCCAAGGCACTGATAGCAGCCACAAGAAAGGCGGCTCCTATTG

Note there are 3 copies of seq1 and two copies of seq2. I want to get a new file that contain only one copy of seq1, seq2, seq3 and seq4.

Thanks

Last edited by vgersh99; 09-05-2018 at 05:20 PM.. Reason: code tags, please!

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bp_search2tribe

BP_SEARCH2TRIBE(1p)					User Contributed Perl Documentation				       BP_SEARCH2TRIBE(1p)

NAME

       search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix

SYNOPSIS

       Usage:
	 search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..

DESCRIPTION

       This script is probably too slow for most people's uses.  It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output
       from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs and then feed the table into MCL
       with the mcxdeblast script and the --m9 option.

       This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering.

       The options are:

	  -o filename	       - the output filename [default STDOUT]
	  -f format	       - search result format (blast, fasta)
				 (ssearch is fasta format). default is blast.
	  -w or --weight VALUE - Change the default weight for E(0.0) hits
				 to VALUE (default=200 (i.e. 1e-200) )
	  -h		       - this help menu

       Additionally specify the filenames you want to process on the command-line.  If no files are specified then STDIN input is assumed.  You
       specify this by doing: search2tribe < file1 file2 file3

AUTHOR

       Jason Stajich, jason-at-bioperl-dot-org

perl v5.14.2							    2012-03-02						       BP_SEARCH2TRIBE(1p)