batch_cnv_blast2gff.pl - Convert blast output to gff format
This documentation refers to program version $Rev: 299 $
batch_cnv_blast2gff.pl -i InDir -o OutDir
-i, --indir # Directory of fasta files to process
-o, --outdir # Path to the base output directory
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.
Path of the directory containing the sequences to process.
Path of the directory to place the program output.
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 results to existing gff file.
Print a short overview of how to use program from the command line.
Print a short program usage state with a summary of options.
Show program version. This will print the SVN version of the script.
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 with maximum output to the screen. This will provided a
detailed status of the progress of the program.
Error messages generated by this program and possible solutions are listed
- 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.
This program does not depend on any configuration files or environmental
- Limited to NCBI BLAST
The current version is limited to using the NCBI version of BLAST.
- 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>
VERSION: $Rev: 299 $