length_seq

#summary Determines the length of each sequence in the stream.

Biopiece: length_seq

Description

[length_seq] determines the length of each sequence in the stream and add this to the SEQ_LEN key.

Usage

... | length_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 file         -  Default=STDOUT
[-v         | --verbose]            #  Verbose output.

Examples

Consider the following table in the file test.tab:

#SEQ_NAME	SEQ
test1	ACGACGAGCATGCA
test2	ACGACTACCTG

We can read in this table using [read_tab] and then pipe the stream though [length_seq]:

read_tab -i test.tab | length_seq 

SEQ: ACGACGAGCATGCA
SEQ_NAME: test1
SEQ_LEN: 14
---
SEQ: ACGACTACCTG
SEQ_NAME: test2
SEQ_LEN: 11
---

See also

[read_tab]

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

[length_seq] is part of the Biopieces framework.

http://www.biopieces.org