write_454

Biopiece: write_454

Description

Usage

... | write_454 [options] -o <FASTA file> -q <QUAL file>

Options

[-?         | --help]               #  Print full usage description.
[-x         | --no_stream]          #  Do not emit records.
[-o <file>  | --data_out=<file>]    #  Write sequences to file.
[-q <file>  | --qual_out=<file>]    #  Write quality scores to file.
[-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

To write the following entry to files:

SCORES: IIIIIIIFFC::::88AEIA@@>>BCCCC/////@99@A:9<;EIIIIIIIIIIIIIIIIIII
SEQ: ACGTCATGGGCAATCCTGAGCCAACTCATGGAAATGGATAGGTGCAGAGACTCAATGGCTGAC
SEQ_NAME: GG42H5Y01A9ZDB rank=0000022 x=406.5 y=2493.0 length=63
---

Do

... | write_454 -o test.fna -q test.qual -x

And obtain the two files with the content:

cat test.fna
>GG42H5Y01A9ZDB rank=0000022 x=406.5 y=2493.0 length=63
ACGTCATGGGCAATCCTGAGCCAACTCATGGAAATGGATAGGTGCAGAGACTCAATGGCTGAC

cat test.qual
>GG42H5Y01A9ZDB rank=0000022 x=406.5 y=2493.0 length=63
40 40 40 40 40 40 40 37 37 34 25 25 25 25 23 23 32 36 40 32 31
31 29 29 33 34 34 34 34 14 14 14 14 14 31 24 24 31 32 25 24 27
26 36 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40

See also

[read_454]

write_fasta

Author

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

[email protected]

May 2010

License

GNU General Public License version 2

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

Help

[write_454] is part of the Biopieces framework.

http://www.biopieces.org