| seq_oligocount.pl |
seq_oligocount.pl - Count oligos from an input sequence
This documentation refers to program version $Rev: 606 $
seq_oligocount.pl -i InFile -o OutDir -db index.fasta
-n SeqName -k 20
-i,--infile # Path to the input fasta file
-d,--db # Path to the mkvtree index file
-o,--outdir # Path to the base output directory
-n,--name # Name to assign to the sequence file
-k,--kmer # Oligomer query length
The seq_oligocount program will take a query sequence, break it into subsequences of size k and query it against an persistent index created by the mkvtree program. It produces a GFF output file describing the number of copies of every oligomer in the query sequence in the subject index database.
Path of the input file.
Path of the output file.
Name to assign to the sequence file
Path to the fasta file that was indexed with the mkvtree program.
Length of the kmer to index. The default value of this variable is 20.
Length of window for summarizing kmer index counts. This will be a non overlapping window and can range from 1 to the length of the sequence.
The name of the sequence being annotated. This is the first column of data in 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.
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.
An external configuration file is not required for this program, and it does not make use of any variables set in the user's environment.
This program requires the Vmatch package of programs. http://www.vmatch.de . This software is availabe at no cost for noncommercial academic use. See program web page for details.
This module is required to copy the BLAST results.
This module is required to accept options at the command line.
The Bio:SeqIO module is a component of the BioPerl package
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
Since this program will generate a large file of your original sequence broken into oligomers, you are somewhat limited to the size of query sequence that is feasible to use this program with.
The output for this program is currently limited to GFF file of points with the copy number of each oligomer designeated.
The seq_oligocount.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: 10/11/2007
UPDATED: 03/24/2009
VERSION: $Rev: 606 $
| seq_oligocount.pl |