NAME

cnv_ta2ap.pl - Convert TriAnnot GFF3 files to Apollo format

SYNOPSIS

Usage

    cnv_ta2ap.pl -i InFastaFile -g GffDir -o OutputDir

Required Arguments

    -g, --gffdir   # Directory containing TriAnnot gff files
    -o, --outdir   # Path to the base output directory

DESCRIPTION

Converts gff data tracks from gff format to the game xml format for use in the Apollo Genome Annotation Curation program. This is for use with output from the TriAnnot pipeline.

REQUIRED ARGUMENTS

-g,--gffdir: This is the directory that contains the gff output from the TriAnnot program that you want to convert.
-o,--outdir: Path of the directory to place the program output.

OPTIONS

--catout: Optional path to a single gff output file that will contain all of the converted files concatenated into a single gff file.
-i,--infile: Input FASTA file. The input fasta file will be used as the base file to map gff sequence features onto when converting from gff to game.xml output.
--ap-path: Full path to the binary file for the Apollo Genome Annotation Curation program.
--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.
--verbose: Run the program with maximum output.
-q,--quiet: Run the program with minimal output.

DIAGNOSTICS

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.