write_solid

Biopiece: write_solid

Description

write_solid writes sequence from the data stream in SOLID format which is a color space model where each color can be one of two residues. Otherwise the format is identical to FASTA format (see write_fasta).

For more about the SOLID:

http://solid.appliedbiosystems.com/

Usage

... | write_solid [options]

Options

[-?         | --help]               #  Print full usage description.
[-x         | --no_stream]          #  Do not emit records.
[-o <file>  | --data_out=<file>]    #  Write result to file.
[-w <uint>  | --wrap=<uint>]         #  Wrap sequences to a given width.
[-I <file!> | --stream_in=<file!>]  #  Read input from stream file  -  Default=STDIN
[-O <file>  | --stream_out=<file>]  #  Write output to stream file  -  Default=STDOUT
[-Z         | --compress]           #  Compress output using gzip.
[-v         | --verbose]            #  Verbose output.

Examples

Consider the following FASTA entry in the file test.fna:

>test
AAATGACTGCTAGTC

To read the entry we use read_fasta and to write as SOLID we use write_solid:

read_fasta -i test.fna | write_solid -x

>test
A00312121323212

See also

read_solid

read_fasta

write_fasta

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

write_solid is part of the Biopieces framework.

http://www.biopieces.org