NAME - Convert LTR_STRUC report output files to gff


This documentation refers to program version $Rev: 596 $


Usage -i InDir -o OutDir -r LStrucOut

Required Arguments

    --indir         # Directory with the fasta files
                    # This is used to find the root seq names
    --outdir        # Directory for the base output dir
    --results       # Directory containing the LTR_STRUC results


Given a directory containing the output from LTR_STRUC and a directory containing the fasta files that the structural predictions were made from,



Path of the intput directory containing the fasta files that were analyzed by LTR_STRUC. It may seem awkward to need to provide this directory of fasta files, but it is currently necessary to be able to find the reports for that sequence set. LTR_Struc does not provide the sequence name in a format that can be parsed. Furthermore, LTR_struc does not provide the location of the sequence features on the sequence file, so the fasta file is needed to map the LTR retrotransposon model back onto the sequence file.


Path of the output directory that will serve as the base for the output from the conversion to gff. Every sequence will have a subdirectory created in this parent dir.


Path of the directory containing the results from LTR_STRUC. It is expected that these file names will end with rprt.txt.



Specify the program name to use in the GFF output file. By default, the program name used is ltr_sturc


Specify the parameter set name to used. This will be appended to the program name in the source column of 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.


Error messages generated by this program and possible solutions are listed below.

ERROR: No fasta files were found in the input directory

The input directory does not contain fasta files in the expected format. This could happen because you gave an incorrect path or because your sequence files do not have the expected *.fasta extension in the file name.

ERROR: Could not create the output directory

The output directory could not be created at the path you specified. This could be do to the fact that the directory that you are trying to place your base directory in does not exist, or because you do not have write permission to the directory you want to place your file in.


The program does not currently require an external configuration file or make use of variables defined in the user's environment.


Required Software

Required Perl Modules




The program is part of the DAWG-PAWS package of genome annotation programs. See the DAWG-PAWS web page ( ) or the Sourceforge project page ( ) 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.




James C. Estill <JamesEstill at>


STARTED: 09/25/2007

UPDATED: 03/24/2009

VERSION: $Rev: 596 $