write_gff

Biopiece: write_gff

Description

write_gff write features from the data stream in GFF format (Generic Feature Format ver 3).

Biopiece records containing the 9 keys required in the GFF format will be output:

1. Q_ID
2. SOURCE
3. TYPE
4. Q_BEG
5. Q_END
6. SCORE
7. STRAND
8. PHASE
9. ATT

Moreover, the keys beginning with ATT_ will be compiled correctly as a list of tag=value pairs that constitutes the attribute field.

STRAND: +
ATT_ID: cds00004
Q_ID: ctg123
SCORE: .
TYPE: CDS
Q_BEG: 3391
Q_END: 3902
PHASE: 0
ATT_PARENT: mRNA00003
SOURCE: .
---

For more about the GFF format:

http://www.sequenceontology.org/resources/gff3.html

Usage

... | write_gff [options]

Options

[-?         | --help]               #  Print full usage description.
[-x         | --no_stream]          #  Do not emit records.
[-o <file>  | --data_out=<file>]    #  Write result 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

See also

read_gff

Author

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

mail@maasha.dk

October 2009

License

GNU General Public License version 2

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

Help

write_gff is part of the Biopieces framework.

http://www.biopieces.org