| cnv_tenest2gff.pl |
cnv_tenest2gff.pl - Convert TENest output to GFF
This documentation refers to program version $Rev: 602 $
cnv_tenest2gff.pl -i infile.txt -o outfile.gff
-i,--infile # Path to the TE Nest result to convert
# Expects input from standard input otherwise
-o,--outfile # Path to the gff format outfile
# Writes output to standard output otherwise
Converts TE Nest output to gff format output. The gff file will label these features as 'exon' to make them compatible with the apollo genome annotation curation program.
The following arguments are the most useful in using the cnv_tenest2gff.pl program. They are not actually required since the cnv_tenest2gff.p program will attempt to use a default name or path that makes sense.
Path of the input file to convert. If an input file is not provided, the program will expect input from STDIN.
Path of the gff formatted output file that . If an output path is not provided, the program will write output to STDOUT.
The sequence name to use in the GFF output file. Otherwise, this will just use 'seq' as the sequence name.
The program used to generate the annotation result. This data is written to the second colum in the gff output file. Be default this value is set to be ``tenest''.
The name of the paramter set used. This will be appened to the data in the second column, and can be used to distinguish among parameter combinations for multiple applications of TE Nest to the same sequence file.
The name to use for the feature type. This is the output value in the third colum of the gff output file. Be default this value is set to ``transposable_element''.
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 error message that can be generated will be listed here.
This program does not make use of a configuration file or variables set in the user's environment.
This program requires output from the TE Nest web server, or from a local copy of the TE nest program. The TE Nest web query is available at: http://www.plantgdb.org/prj/TE_nest/TE_nest.html. You can download the TE nest program at: http://www.public.iastate.edu/~imagefpc/Subpages/software.html.
If you find a bug with this software, file a bug report on the DAWG-PAWS Sourceforge website: http://sourceforge.net/tracker/?group_id=204962
If you find a limitation that makes it difficult to use this program, please file a bug report on the DAWG-PAWS Sourceforge website: http://sourceforge.net/tracker/?group_id=204962
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. http://dawgpaws.sourceforge.net/
GNU LESSER GENERAL PUBLIC LICENSE
GNU General Public License, Version 3
http://www.gnu.org/licenses/gpl.html
THIS SOFTWARE COMES AS IS, WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. USE AT YOUR OWN RISK.
James C. Estill <JamesEstill at gmail.com>
STARTED: 08/27/2007
UPDATED: 03/24/2009
VERSION: $Rev: 602 $
| cnv_tenest2gff.pl |