| cnv_ltrfinder2gff.pl |
cnv_ltrfinder2gff.pl - Converts LTR_Finder output to gff format
This documentation refers to program version $Rev: 594 $
cnv_ltrfinder2gff.pl -i lf_result.txt -o lf_result.gff
--infile # Path to the input file
# Result from a single record fasta file
--outdir # Base output dir
Convert the ltrfinder output to gff format. This assumes that the output from ltr_finder correspons to a single BAC. A suffix can be passed with the --suffix option to provide a suffix for the source column. For example run default ltr_finder results with --suffix def to create ltr_finder:def. T
Path of the input file. If an input file is not provided, the program will expect input from STDIN.
Path of the output file. 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 name of the paramter set used. This will be appened to the data in the second column of the GFF file, and can be used to distinguish among parameter combinations for multiple applications of ltrfinder to the same sequence file.
Append the GFF output to the gff file indicate by the --outfile option. This allows you to append results from multiple programs to a single GFF file, but it is generally recommended to create separate GFF files and concatenate them at a later stage.
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.
Error messages that you may encounter and possible solutions are listed below:
If a file is not specified by the -i or --infile option, the program will expect to receive intput from standard input.
This program does not make use of a configuartion file or variables set in the user's environment.
This program requires the following software:
This program parses output from the LTR finder program. It is possible to obtain a linux binary by contacting the authors : xuzh <at> fudan.edu.cn. It is also possible to obtain these results using the LTR_FINDER web page: http://tlife.fudan.edu.cn/ltr_finder/
This program does not make use of perl modules beyond those installed with the basic Perl package. If you discover a dependency that is not documented here, please email the author or file a bug report.
Any known bugs and limitations will be listed here.
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
This program is known to parse the results from LTR_FINDER v 1.0.2. This program has not been tested with the results from the LTR_FINDER web site.
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 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: 09/14/2007
UPDATED: 03/24/2009
VERSION: $Rev: 594 $
| cnv_ltrfinder2gff.pl |