| cnv_seq2dir.pl |
cnv_seq2dir.pl - Split sequence file to dir of seq files
This documentation refers to program version $Rev: 582 $
cnv_seq2dir.pl -i infile.fasta -f fasta -o dir [-r name]
--infile # Path to the input file
# Expects STDIN if not specified
--format # Format of the sequence file
# (fasta|genbank)
--outdir # Path to the output directory
--rootname # Base name for output files
# Uses seq id if not specified
Takes an input file in any valid bioperl format and converts it to a directory containing one fasta file for each sequence. Files are placed in a subdirectory under the current working directory that is given the same name as the outfile prefix.
The input file containing multiple sequence records to split into single sequence files.
The directory to place all of files with the single sequence records in. If this option is not specified. The sequences will be placed in a subdirectory of the current working directory named ind_seq_out.
A root name to serve as the individual names of the output files. These will have a running number suffix appended to the outfile name. If not specified, the primary id on the input record will be used to name the output files.
An integer representing the number of digits to pad file names with. This will be used to append to file names when the --rootname option is used. For example, this will transfrom root_1 to root_0001. The default is not to pad the numbers.
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 maximum output.
Run the program with minimal output.
The program could not create the directory needed to hold the output for the sequence file. It is possible that you not have the proper access to create a directory in the path that you specified. It is also possible that the directory that you are trying to create this subdirectory in does not exist.
This program does not make use of a configuration file or options set in the user's environment.
This program does not required any additional software.
This module is required to read the sequence files in and to write the sequence files out.
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 a limitation to your use of this software please email the author or file a bug report at the DAWG-PAWS sourceforge website: http://sourceforge.net/tracker/?group_id=204962
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: 07/22/2004
UPDATED: 03/24/2009
VERSION: $Rev: 582 $
| cnv_seq2dir.pl |