analyze_gc

Biopiece: analyze_gc

Description

analyze_gc analyzes the sequence specified by the SEQ key in each record and adds a GC% key with the percentage GC composition of that particular sequence.

For more complex sequence analysis use analyze_seq.

Usage

... | analyze_gc [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 file test.fna containing the single entry:

>test
ACGACGCATNNNNNNactgatcga

To analyze this sequence, read the file using read_fasta:

SEQ_NAME: test
GC%: 37.50
SEQ: ACGACGCATNNNNNNactgatcga
SEQ_LEN: 24
---

If you have a stack of sequences in one file and you want to determine the mean GC content of all the sequences, you can do it using the mean_vals biopiece:

read_fasta -i test.fna | analyze_gc | mean_vals -k GC% -x

GC%_MEAN: 37.50
---

See also

read_fasta

analyze_seq

mean_vals

Author

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

[email protected]

August 2009

License

GNU General Public License version 2

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

Help

analyze_gc is part of the Biopieces framework.

http://www.biopieces.org