| fetch_tenest.pl |
fetch_tenest.pl - Fetch TE Nest LTR and SVG files
This documentation refers to $Rev: 584 $
fetch_tenest.pl -c SeqList.txt -o OutDir [--gff]
-c, --config # Path to the config file
-o, --outdir # Path to the base output directory
--gff # Convert output to GFF files
Given a tab delimited input file of theFetches the TE Nest results using wget. The results are converted to gff and copied to the gff dir if requested.
Path of the configuration file. This is a tab delimited input file that must be in the following format:
HEX0350E24 1188334554_18873
HEX0358K19 1188334578_19208
HEX0411K13 1188334604_19821
Where the first column is the name of the sequence that was analyzed by TE Nest and the second column is the id of the TE Nest job. This job id is returned by TE Nest when the job is initially submitted.
Path of the output directory. This is the base dir that the analysis results are stored in.
Convert downloaded data to the GFF file format.
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.
The configuration file used by fetch_tenest.pl a tab delimited text file that must be in the following format:
HEX0350E24 1188334554_18873
HEX0358K19 1188334578_19208
HEX0411K13 1188334604_19821
Where the first column is the name of the sequence that was analyzed by TE Nest and the second column is the id of the TE Nest job. This job id is returned by TE Nest when the job is initially submitted.
The fetch_tenest.pl program does not currently make use of variables defined in the user's environment.
As of 12/12/2007 the only way to use the TE Nest program is through a web service provided by the Plant GDB web site http://www.plantgdb.org/prj/TE_nest/TE_nest.html
This module is required to copy the BLAST results.
This module is required to accept options at the command line.
This module is a simple interface to fetching files over the web. This is used to fetch results from the TE Nest web server.
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
The config file must have UNIX formatted line endings. Because of this any config files that have been edited in programs such as MS Word must be converted to a UNIX compatible text format before being used with batch_blast.
The fetch_tenest.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
James C. Estill <JamesEstill at gmail.com>
STARTED: 08/29/2007
UPDATED: 12/12/2007
VERSION: $Rev: 584 $
| fetch_tenest.pl |