Batch_cnv_ta2ap.pl - Convert TriAnnotation to Apollo GFF
This documentation refers to batch_cnv_ta2ap.pl version $Rev$
batch_cnv_ta2ap.pl -i DirToProcess -o OutDir
-i, --indir # Directory of fasta files to process
-o, --outdir # Path to the base output directory
Converts TriAnnotation program output to a GFF format that is
compatible with the Apollo Genome Annotation Curation program.
Path of the directory containing the sequences to process.
Path of the directory to place the program output.
The path to the Apollo Genome Annotation curation program. This is the
executable binary for the program that can accept command line options.
Path to a file that will be used to log program status.
If the file already exists, additional information will be concatenated
to the existing file.
Use the apollo program to convert the file from gff to game xml.
The default is not to use apollo.
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.
Run the program without doing the system commands.
Error messages generated by this program and possible solutions are listed
- 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.
This program does not depend on any configuration files or environmental
This module is required to copy the BLAST results.
This module is required to accept options at the command line.
- Limited file extensions are supported
BLAST output file must currently end with blo, bln, or blx. For example
a BLASTx output may be named BlastOut.blx while a BLASTN output
may be names BlastOut.bln. FASTA files must end with a fasta or fa extension.
For examples must have names like my_seq.fasta or my_seq.fa.
The batch_blast.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.
GNU GENERAL PUBLIC LICENSE, VERSION 3
James C. Estill <JamesEstill at gmail.com>