| cnv_findmite2gff.pl |
cnv_findmite2gff.pl - Convert FINDMITE output to gff format
This documentation refers to program $Rev: 527 $
cnv_findmite2gff -i InFile -o GffOutFile [-f FastaOutFile]
-i # Path to the Findmite result to convert
# If not specified, the program will expect input from STDIN
-o # Path to the gff format output file
# If not specified the program will write output to STDOUT
Converts FINDMITE output to GFF format. May also be used to extract the MITEs from to a FASTA file by using the --fasta option.
Path of the input file that contains the results of the FINDMITE program. If this option is not specified, the program will expect input from STDIN.
Path to the gff output file. If and outfile file path is not specified, the program will write the output to STDERR.
The parameter name to append to the source program name. This information will be appended to the second column of the gff output file. This is used to specify the parameter set used to generate the FINDMITE results.
The program name to use. This is the data in the second column of the gff output file. Be default, this is set to 'findmite'. This option allows you to specify other program names if desired.
Identifier for the sequence file that was masked with repeatmasker. The out file from repeatmasker may have truncated your original file name, and this option allows you to use the full sequence name.
Genreate a fasta format output file. This file will contain the putative MITEs.
Append the gff data to the any existing data in the file specified by -o,--outfile.
Append the MITE fasta file data to any existing data in the file specified by -f,fasta.
Run the program with minimal output.
Run the program in verbose mode.
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.
The error messages that can be generated will be listed here.
You will see this message if you did not specify an input file with the -i or --input options.
This program does not make use of a configuration file or variables set in the user environment.
Other modules or software that the program is dependent on.
This program requires the FINDMITE program. This program is available as an executable for Unix based operating systems at: at http://jaketu.biochem.vt.edu/dl_software.htm
This program does not make use of Perl modules outside of the normal suite of modules present in a typical installation of perl.
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 discover limitations with your use of this software, please file a bug report on the DAWG-PAWS Sourceforge website: http://sourceforge.net/tracker/?group_id=204962
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: 08/30/2007
UPDATED: 02/03/2009
VERSION: $Rev: 527 $
| cnv_findmite2gff.pl |