If the filename is given as - then the input is taken from
standard input. Compressed files (.gz, .Z, .bz2) are automatically
FASTA format files are distinguished from GFF files by their filename
extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as FASTA files. Everything else is
treated as a GFF file. If you wish to load -fasta files from STDIN,
then use the -f command-line swith with an argument of -, as in
gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -
The nature of the load requires that the database be on the local
machine and that the indicated user have the file privilege to load
the tables and have enough room in /usr/tmp (or whatever is specified
by the \$TMPDIR environment variable), to hold the tables transiently.
If your MySQL is version 3.22.6 and was compiled using the load local
file option, then you may be able to load remote databases with local
data using the --local option.
About maxfeature: the default value is 100,000,000 bases. If you have
features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000. This value
must be a power of 10.
If the list of GFF or fasta files exceeds the kernel limit for the
maximum number of command-line arguments, use the
--long_list /path/to/files option.
The adaptor used is dbi::mysqlopt. There is currently no way to