NAME - Segment and parse a large gff file


This documentation refers to program version $Rev: 589 $


=head2 Usage -i infile.gff -s seg_out.gff -p par_out.gff -t integer

Required Arguments

    -i,--infile         # Path to the input file
    -s,--seg-out        # Path to the segmented output file
    -p,--parse-out      # Path to the parsed output file
    -t,--thresh         # Threshold value


Given a gff file that contains point or segement data will extract segments that exceed a threshold value or array of threshold values. Will create a gff segment file as well as a gff parse file. The segment file converts the vals to segments that meet the threshold criteria while the parse file returns all points or segments in the input file that exceed the threshold value.



Path of the input file.


Gff file of the segmented data


Gff file of the parsed data. This will include all rows in the original file that exceed the threshold value.


Threshold value. A single integer that represents the threshold value. The output will return all features that are greater then or equal to the threshold value.



The program used to generate the gff result. This is the value in the second column of the GFF file. By default, the program name used in the original GFF file will be used.


The parameter used to generate the segmentation. For example, 20mer_100x for 20mer oligos with a threshold value of 100x coverage.


The name of the sequence file being annotated. This is the first column of data in the gff output file.


Short overview of how to use program from command line.


Show program usage with summary of options.


Show program version.


Show the full program manual. This uses the perldoc command to print the POD documentation for the program.


Run the program with minimal output.


The list of error messages that can be generated, explanation of the problem one or more causes suggested remedies list exit status associated with each error


Names and locations of config files environmental variables or properties that can be set.


Other modules or software that the program is dependent on.


Any known bugs and limitations will be listed here.


A manuscript is being submitted describing the DAWGPAWS program. Until this manuscript is published, please refer to the DAWGPAWS SourceForge website when describing your use of this program:

JC Estill and JL Bennetzen. 2009. The DAWGPAWS Pipeline for the Annotation of Genes and Transposable Elements in Plant Genomes.


GNU General Public License, Version 3


James C. Estill <JamesEstill at>


STARTED: 02/17/2008

UPDATED: 03/25/2009

VERSION: $Rev: 589 $