BP_LOAD_GFF(1p)

💖 BP_LOAD_GFF 💖

okay bestie, so this whole thing is about bp_load_gff.pl — and what it does is load a Bio::DB::GFF database from GFF files. that's it, that's the job. ✨

(the manual page calls it BP_LOAD_GFF(1p) and honestly she's giving very "Perl user-contributed docs" energy, which, slay.)

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🌸 SYNOPSIS 🌸

% bp_load_gff.pl -d testdb -u user -p pw
   --dsn 'dbi:mysql:database=dmel_r5_1;host=myhost;port=myport'
      dna1.fa dna2.fa features1.gff features2.gff ...

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🦋 DESCRIPTION 🦋

okay so this script fills up a Bio::DB::GFF database with all the features sitting inside a list of GFF files and/or FASTA sequence files. and when I say GFF I mean you HAVE to use the exact variant of GFF that's described in Bio::DB::GFF — no improvising, no freestyling, she's specific like that. 💅

then there's a whole bunch of command-line options that let you pick which database to load and decide whether an existing database is allowed to be overwritten or not.

this script talks through the Bio::DB::GFF interface, so it works with every database adaptor that module currently supports (MySQL, Oracle, PostgreSQL soon 👀). but bestie... it's slow. like, lowkey tragic. if you want faster loading, go look at the MySQL-specific bp_bulk_load_gff.pl and bp_fast_load_gff.pl scripts instead. they're the main characters of loading speed fr fr. 🔥

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📝 NOTES 📝

if you hand it a filename of - then the input gets taken from standard input. and compressed files (.gz, .Z, .bz2) get uncompressed automatically for you — she does it herself, no extra steps. 🫶

FASTA format files get told apart from GFF files by their filename extensions. so files ending in .fa, .fasta, .fast, .seq, .dna — plus all their uppercase variants — get treated as FASTA files. everything else gets treated as a GFF file. no exceptions, no vibes-based guessing.

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 -

⚠️ heads up: on the first load of a database you're gonna see a bunch of "unknown table" errors. that is normal. do not panic, do not spiral, it's just how the first load goes. 💀

about maxfeature: the default value is 100,000,000 bases. so 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, or another power of 10. 👑

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✨ COMMAND-LINE OPTIONS ✨

command-line options can be abbreviated down to single-letter options. e.g. -d instead of --database. yes bestie, she's flexible like that. 💅

• --dsn <dsn> — the data source (default dbi:mysql:test)
• --adaptor <adaptor> — the schema adaptor (default dbi::mysqlopt)
• --user <user> — username for mysql authentication
• --pass <password> — password for mysql authentication
• --fasta <path> — fasta file, or a directory containing fasta files, for the DNA
• --create — force creation and initialization of the database
• --maxfeature — set the value of the maximum feature size (default 100 Mb; 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
• --upgrade — upgrade an existing database to the current schema
• --gff3_munge — activate GFF3 name munging (see Bio::DB::GFF)
• --quiet — no progress reports
• --summary — generate summary statistics for drawing coverage histograms. this can be run on a previously loaded database or during the load.

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🌈 SEE ALSO 🌈

Bio::DB::GFF, bulk_load_gff.pl, bp_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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okay that's the whole page bestie, you ate it, go load some GFF files 💖✨

perl v5.30.0 · 2020-01-13 · mwah, that's the tea 🎀🦋