NAME

batch_cnv_blast2gff.pl - Convert blast output to gff format

VERSION

This documentation refers to program version $Rev: 299 $

SYNOPSIS

Usage

    batch_cnv_blast2gff.pl -i InDir -o OutDir

Required Arguments

    -i, --indir    # Directory of fasta files to process
    -o, --outdir   # Path to the base output directory

DESCRIPTION

Convert NCBI BLAST output to an Apollo compatible GFF file. This can produce a separate gff file for each BLAST report, or can merge all BLAST results into a single GFF file.

REQUIRED ARGUMENTS

-i,--indir: Path of the directory containing the sequences to process.
-o,--outdir: Path of the directory to place the program output.

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
--append: Append results to existing gff file.
--usage: Print a short overview of how to use program from the command line.
--help: Print a short program usage state with a summary of options.
--version: Show program version. This will print the SVN version of the script.
--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.
--verbose: Run the program with maximum output to the screen. This will provided a detailed status of the progress of the program.

DIAGNOSTICS

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

ERROR: No fasta files were found in the input directory: The input directory does not contain fasta files in the expected format. This could happen because you gave an incorrect path or because your sequence files do not have the expected *.fasta extension in the file name.
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.