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shuffle_seq
Martin Asser Hansen edited this page Oct 2, 2015
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shuffle_seq shuffles the residue order within each sequence in the stream. The shuffling is completely random and there is no need for additional piping of the stream through shuffle_seq.
... | shuffle_seq [options]
[-? | --help] # Print full usage description.
[-I <file!> | --stream_in=<file>!] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following FASTA entry in the file test.fna:
>test
ACGACGCATNNNNNNactgatcga
To shuffle the sequence do:
read_fasta -i test.fna | shuffle_seq
SEQ: NcNNCAgaCNANGATattNgCGac
SEQ_NAME: test
SEQ_LEN: 24
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Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
shuffle_seq is part of the Biopieces framework.