swapcase_seq

Biopiece: swapcase_seq

Description

swapcase_seq changes all lowercase sequence to uppercase and visa versa for all sequences in the stream.

Usage

... | swapcase_seq [options]

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.

Examples

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
---

See also

read_fasta

lowercase_seq

uppercase_seq

transliterate_seq

transliterate_vals

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

[email protected]

August 2010

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

swapcase_seq is part of the Biopieces framework.

http://www.biopieces.org