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BP_FAST_LOAD_GFF(1)   User Contributed Perl Documentation  BP_FAST_LOAD_GFF(1)

       bp_fast_load_gff.pl - Fast-load a Bio::DB::GFF database from GFF files.

	 % bp_fast_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...

       This script loads a Bio::DB::GFF database with the features contained
       in a list of GFF files and/or FASTA sequence files.  You must use the
       exact variant of GFF described in Bio::DB::GFF.	Various command-line
       options allow you to control which database to load and whether to
       allow an existing database to be overwritten.

       This script is similar to load_gff.pl, but is much faster.  However, it
       is hard-coded to use MySQL and probably only works on Unix platforms
       due to its reliance on pipes.  See bp_load_gff.pl for an incremental
       loader that works with all databases supported by Bio::DB::GFF, and
       bp_bulk_load_gff.pl for a fast MySQL loader that supports all

       If the filename is given as "-" then the input is taken from standard
       input. Compressed files (.gz, .Z, .bz2) are automatically uncompressed.

       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 change

       Command-line options can be abbreviated to single-letter options.  e.g.
       -d instead of --database.

	  --database <dsn>	Mysql database name
	  --create		Reinitialize/create data tables without asking
	  --local		Try to load a remote database using local data.
	  --user		Username to log in as
	  --fasta		File or directory containing fasta files to load
	  --password		Password to use for authentication
	  --long_list		Directory containing a very large number of
				GFF and/or FASTA files
	  --maxfeature		Set the value of the maximum feature size (default 100Mb; must be a power of 10)
	  --group		A list of one or more tag names (comma or space separated)
				to be used for grouping in the 9th column.
	  --gff3_munge		Activate GFF3 name munging (see Bio::DB::GFF)
	  --summary		Generate summary statistics for drawing coverage histograms.
				  This can be run on a previously loaded database or during
				  the load.
	  --Temporary		Location of a writable scratch directory

       Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl

       Lincoln Stein, lstein@cshl.org

       Copyright (c) 2002 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it
       under the same terms as Perl itself.  See DISCLAIMER.txt for
       disclaimers of warranty.

perl v5.20.2			  2015-09-15		   BP_FAST_LOAD_GFF(1)

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