| cnv_findltr2gff.pl |
cnv_findltr2gff.pl - Convert output from find_ltr.pl to gff format.
This documentation refers to version $Rev: 593 $
cnv_findltr2gff.pl -i infile.ltrpos -o outfile.gff [--seqname HEX451]
-i # Path to the ltrpos input file
# Defaults to STDIN if not specified
-o # Path to the gff format output file
# Defaults to STDOUT if not specified
-s # Identifier for the annotated sequence
-p # Name of use as a suffix in the gff source column
# This is generally the parameter set used
Converts output from the find_ltr.pl ltr annotation program to the standard gff format. The find_ltr.pl program is a component of the LTR DeNovo package ( http://darwin.informatics.indiana.edu/evolution/LTR.tar.gz ) described in Rho, M., J. H. Choi, et al. (2007). BMC Genomics 8: 90.
Path of the input file. This is a computational result from the find_ltr.pl program. 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 program name used to produce the computational prediction. By default this is set to be 'FindLTR'.
Name to use as the suffix when naming the source in the gff output. This can be used to distinguish among find_ltr runs that used different paramater sets. This will be append to findltr: to produce a name that can be unique for each parameter set result. For example the default parameter set could be given a def suffix while and alternate paramater set could be given the suffix alt. This will produce gff source lines of findltr:def and findltr:alt.
The name of the sequence that is being annotated. This is placed in the first field of the gff output 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.
Run the program with minimal output.
Run the program in verbose mode.
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 configuration file or variables set in the user's environment.
The following software is required for this program:
This program is designed to parse output from the ltr_finder.pl program. http://darwin.informatics.indiana.edu/evolution/LTR.tar.gz
M Rho et al. 2007. 'De novo identificatio of LTR retrotransposons in eukaryotic genomes' BMC Genomics 8:90.
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 can parse results generated by the find_ltr.p program as downloaded from http://darwin.informatics.indiana.edu/evolution/LTR.tar.gz in 2008.
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.
STARTED: 09/13/2007
UPDATED: 01/29/2009
VERSION: $Rev: 593 $
| cnv_findltr2gff.pl |