NAME

Batch_cnv_ta2ap.pl - Convert TriAnnotation to Apollo GFF

VERSION

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.

--ap-path: The path to the Apollo Genome Annotation curation program. This is the executable binary for the program that can accept command line options.
--logfile: 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.
--apollo: Use the apollo program to convert the file from gff to game xml. The default is not to use apollo.
--usage: Short overview of how to use program from command line.
--help: Show program usage with summary of options.
--version: Show program version.
--man: Show the full program manual. This uses the perldoc command to print the POD documentation for the program.
-q,--quiet: Run the program with minimal output.
--test: Run the program without doing the system commands.

Error messages generated by this program and possible solutions are listed below.

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.