read_gff
Martin Asser Hansen edited this page Oct 2, 2015
·
5 revisions
read_gff reads GFF (Generic Feature Format - version 3) data from one or more files.
For more about the GFF format:
http://www.sequenceontology.org/gff3.shtml
read_gff [options] -i <GFF file(s)>
[-? | --help] # Print full usage description.
[-i <files!> | --data_in=<files!>] # Comma separated list of files or glob expression to read.
[-n <uint> | --num=<uint>] # Limit number of records to read.
[-I <file!> | --stream_in=<file!>] # Read input stream from file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output stream to file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following GFF entries in the file test.gff
##gff-version 3
##sequence-region 2L 204333 23011544
2L FlyBase chromosome_band -204333 1326937 . + . ID=band-21_chromosome_band;Name=band-21;
Reading this file with read_gff results in:
read_gff -i test.gff
STRAND: +
ATT_ID: band-21_chromosome_band
Q_ID: 2L
SCORE: .
TYPE: chromosome_band
ATT_NAME: band-21
Q_BEG: 204334
Q_END: 1326936
ATT: ID=band-21_chromosome_band;Name=band-21;
PHASE: .
SOURCE: FlyBase
---
Notice how the ATT key has been split into key/value pairs that have been added to the record (ADD_ID and ATT_NAME).
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
read_gff is part of the Biopieces framework.