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swapcase_seq
Martin Asser Hansen edited this page Oct 2, 2015
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swapcase_seq changes all lowercase sequence to uppercase and visa versa for all sequences in the stream.
... | swapcase_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 sequence entry in FASTA format in the file test.fna:
>test
ACGACGCATNNNNNNactgatcga
To read in this sequence use read_fasta to change the case for all residues:
read_fasta -i test.fna | swapcase_seq
SEQ: acgacgcatnnnnnnACTGATCGA
SEQ_NAME: test
SEQ_LEN: 24
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Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2010
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
swapcase_seq is part of the Biopieces framework.