| cnv_ltrseq2gff.pl |
cnv_ltrseq2gff.pl - Convert LTR_seq output to GFF format.
This documentation refers to program version $Rev: 595 $
cnv_ltrseq2gff.pl -i InFile -o OutFile -s SeqName
-i,--infile # Directory of fasta files to process
-o,--outfile # Path to the output file
-s,--seqname # ID of the sequence record analyzed
Converts program output from LTR_seq LTR prediction program to GFF format.
Path of the input file which is the prediction results from LTR_seq. If an input file is not specified, the program will expect intput from STDIN.
Path of the output file which will be the GFF output from cnv_ltrseq2gff.pl. If an input file is not specified, the program will print output to STDOUT.
The sequence ID of the query sequence that was analyzed. This will be used to write to the first column of the GFF output file.
Append the GFF results to an existing GFF file. The path to the existing GFF file is indicated by the --outfile option.
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 in verbose mode.
Run the program with minimal output.
Error messages generated by this program and possible solutions are listed below.
The path to the input file you provided by the --infile option may be incorrect, or you do not have permission to read the file that exists at that location.
The directory that you specified at the --outfile option may not exist, or you may not have permission to write files in that directory.
The cnv_ltrseq2gff.pl program does not required an external configuration file or make use of variables defined in the user's environment.
This program requires output from LTR_seq. LTR_seq is available upon email request from the author, Ananth Kalyanaraman: http://www.eecs.wsu.edu/~ananth/contact.htm.
Also see the original publication for the LTR_par program :
A. Kalyanaraman, S. Aluru. 2006. Efficient algorithms and software for detection of full-length LTR retrotransposons. Journal of Bioinformatics and Computational Biology (JBCB), 4(2):197-216.
This module is required to copy the BLAST results.
This module is required to accept options at the command line.
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 currently limited to analyzing results from FASTA files that contain a single record.
The batch_blast.pl program is part of the DAWG-PAWS package of genome annotation programs. See the DAWG-PAWS web page ( http://dawgpaws.sourceforge.net/ ) or the Sourceforge project page ( http://sourceforge.net/projects/dawgpaws ) for additional information about this package.
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: 09/03/2007
UPDATED: 03/30/2009
VERSION: $Rev: 595 $
| cnv_ltrseq2gff.pl |