gmod_gff3_preprocessor.plp - Online in the Cloud

PROGRAM:

NAME

$0 - Prepares a GFF3 file for bulk loading into a chado database.

SYNOPSIS

% gmod_gff_preprocessor [options] --gfffile <filename>

COMMAND-LINE OPTIONS

--gfffile The file containing GFF3 (optional, can read
from stdin)
--outfile The name kernel that will be used for naming result files
--splitfile Split the files into more manageable chunks, providing
an argument to control splitting
--onlysplit Split the files and then quit (ie, don't sort)
--nosplit Don't split the files (ie, only sort)
--hasrefseq Set this if the file contains a reference sequence line
(Only needed if not splitting files)
--dbprofile Specify a gmod.conf profile name (otherwise use default)
--inheritance_tiers How many levels of inheritance do you expect tis file
to have (default: 3)

DESCRIPTION

splitfile -- Just setting this flag to 1 will cause the file to be split by reference
sequence. If you provide an optional argument, it will be further split according to
these rules:

source=1 Splits files according to the value in the source column
source=a,b,c Puts lines with sources that match (via regular expression)
'a', 'b', or 'c' in a separate file
type=a,b,c Puts lines with types that match 'a', 'b', or 'c' in a
separate file

For example, if you wanted all of your analysis results to go in a separate file, you
could indicate '--splitfile type=match', and all cDNA_match, EST_match and
cross_genome_match features would go into separate files (separate by reference sequence).

inheritence_tiers -- The number of levels of inheritance this file has. For example, if
the file has "central dogma" genes in it (gene/mRNA/ exon,polypeptide), then it has 3. Up
to 4 is supported but the higher the number, the more slowly it performs. If you don't
know, 3 is a reasonable guess.

FASTA sequence
If the GFF3 file contains FASTA sequence at the end, the sequence will be placed in a
separate file with the extension '.fasta'. This fasta file can be loaded separately after
the split and/or sorted GFF3 files are loaded, using the command:

gmod_bulk_load_gff3.pl -g <fasta file name>

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