1BP_FAST_LOAD_GFF(1) User Contributed Perl Documentation BP_FAST_LOAD_GFF(1)
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6 bp_fast_load_gff.pl - Fast-load a Bio::DB::GFF database from GFF files.
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9 % bp_fast_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...
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12 This script loads a Bio::DB::GFF database with the features contained
13 in a list of GFF files and/or FASTA sequence files. You must use the
14 exact variant of GFF described in Bio::DB::GFF. Various command-line
15 options allow you to control which database to load and whether to
16 allow an existing database to be overwritten.
17 This script is similar to load_gff.pl, but is much faster. However, it
19 is hard-coded to use MySQL and probably only works on Unix platforms
20 due to its reliance on pipes. See bp_load_gff.pl for an incremental
21 loader that works with all databases supported by Bio::DB::GFF, and
22 bp_bulk_load_gff.pl for a fast MySQL loader that supports all plat‐
23 forms.
24 NOTES
26 If the filename is given as "-" then the input is taken from standard
28 input. Compressed files (.gz, .Z, .bz2) are automatically uncompressed.
29 FASTA format files are distinguished from GFF files by their filename
31 extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their
32 uppercase variants are treated as FASTA files. Everything else is
33 treated as a GFF file. If you wish to load -fasta files from STDIN,
34 then use the -f command-line swith with an argument of '-', as in
35 gunzip my_data.fa.gz ⎪ bp_fast_load_gff.pl -d test -f -
37 The nature of the load requires that the database be on the local
39 machine and that the indicated user have the "file" privilege to load
40 the tables and have enough room in /usr/tmp (or whatever is specified
41 by the \$TMPDIR environment variable), to hold the tables transiently.
42 If your MySQL is version 3.22.6 and was compiled using the "load local
43 file" option, then you may be able to load remote databases with local
44 data using the --local option.
45 About maxfeature: the default value is 100,000,000 bases. If you have
47 features that are close to or greater that 100Mb in length, then the
48 value of maxfeature should be increased to 1,000,000,000. This value
49 must be a power of 10.
50 If the list of GFF or fasta files exceeds the kernel limit for the max‐
52 imum number of command-line arguments, use the --long_list
53 /path/to/files option.
54 The adaptor used is dbi::mysqlopt. There is currently no way to change
56 this.
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59 Command-line options can be abbreviated to single-letter options. e.g.
60 -d instead of --database.
61 --database <dsn> Mysql database name
63 --create Reinitialize/create data tables without asking
64 --local Try to load a remote database using local data.
65 --user Username to log in as
66 --fasta File or directory containing fasta files to load
67 --password Password to use for authentication
68 --long_list Directory containing a very large number of
69 GFF and/or FASTA files
70 --maxfeature Set the value of the maximum feature size (default 100Mb; must be a power of 10)
71 --group A list of one or more tag names (comma or space separated)
72 to be used for grouping in the 9th column.
73 --gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
74 --Temporary Location of a writable scratch directory
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77 Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
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80 Lincoln Stein, lstein@cshl.org
81 Copyright (c) 2002 Cold Spring Harbor Laboratory
83 This library is free software; you can redistribute it and/or modify it
85 under the same terms as Perl itself. See DISCLAIMER.txt for dis‐
86 claimers of warranty.
87perl v5.8.8 2007-05-07 BP_FAST_LOAD_GFF(1)