BP_FAST_LOAD_GFF(1p)

💖 BP_FAST_LOAD_GFF(1p) — or, as the girlies call it, bp_fast_load_gff.pl 💖

okay so welcome to the User Contributed Perl Documentation section bestie, you're in the right place 🌸

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✨ NAME ✨

bp_fast_load_gff.pl — fast-load a Bio::DB::GFF database from GFF files. no cap, it's fast.

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🦋 SYNOPSIS 🦋

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

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🌈 DESCRIPTION 🌈

This script loads a Bio::DB::GFF database with all the features chilling inside a list of GFF files and/or FASTA sequence files. Important: you must use the exact variant of GFF described in Bio::DB::GFF — no improvising, bestie, it's giving ✨specific✨.

You've got various command-line options that let you control which database gets loaded, and whether an existing database is allowed to be overwritten. (Rude of you, but okay 💅)

This script is similar to load_gff.pl, except it's much faster. The catch? It's hard-coded to use MySQL and it probably only works on Unix platforms because it relies on pipes. 🥲 See bp_load_gff.pl for an incremental loader that works with every database supported by Bio::DB::GFF, and bp_bulk_load_gff.pl for a fast MySQL loader that supports all platforms. Options, options, options 👑

💀 NOTES 💀

If the filename is given as - then the input is taken from standard input. Compressed files (.gz, .Z, .bz2) get automatically uncompressed. We love a self-sufficient icon 🫶

FASTA format files are told apart 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. And if you wanna load -fasta files from STDIN, use the -f command-line swith with an argument of '-', like this:

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 has the "file" privilege to load the tables, plus 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. math girlies rise 🧮✨

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. Slay, problem solved 💅

The adaptor used is dbi::mysqlopt. There is currently no way to change this. It said what it said. periodt. 🙈

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👑 COMMAND-LINE OPTIONS 👑

Command-line options can be abbreviated to single-letter options. e.g. -d instead of --database. Short and sweet, main character energy.

• --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

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🔥 SEE ALSO 🔥

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

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💜 AUTHOR 💜

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.

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and that's the whole page bestie ✨ this lil manual was brought to you by perl v5.30.0, dated 2020-01-13, filed under BP_FAST_LOAD_GFF(1p) 💖 mwah, go load some GFF 🎀🦋