uppercase_seq

Biopiece: uppercase_seq

Description

[upppercase_seq] changes all lowercase letter in sequences to uppercase letters.

Usage

... | uppercase_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 uppercase all letters:

read_fasta -i test.fna | uppercase_seq 

SEQ: ACGACGCATNNNNNNACTGATCGA
SEQ_NAME: test
SEQ_LEN: 24
---

See also

[read_fasta]

[lowercase_seq]

[swapcase_seq]

[transliterate_seq]

[transliterate_vals]

Author

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

[email protected]

August 2007

License

GNU General Public License version 2

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

Help

[uppercase_seq] is part of the Biopieces framework.

http://www.biopieces.org