BP_BULK_LOAD_GFF(1p)

💖 BP_BULK_LOAD_GFF 💖

okay so bestie, welcome to the bp_bulk_load_gff.pl page from the User Contributed Perl Documentation section (man page BP_BULK_LOAD_GFF(1p), she's a section 1p girly, very Perl, very iconic) 💅

---

✨ NAME ✨

bp_bulk_load_gff.pl — Bulk-load a Bio::DB::GFF database from GFF files. no cap, that's literally her whole job 🎀

---

🌸 SYNOPSIS 🌸

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

---

🦋 DESCRIPTION 🦋

so this script loads up a Bio::DB::GFF database with all the features chilling inside a list of GFF files and/or FASTA sequence files. it's giving "dump everything in at once" energy 🫶

important, bestie: you must use the exact variant of GFF described in Bio::DB::GFF. no improvising, no freestyling, the format has to match or it's not gonna eat.

there's a bunch of command-line options that let you control which database gets loaded and whether an existing database is allowed to get overwritten (spoiler: overwriting is dramatic and you should be aware).

---

💀 NOTES 💀

if the filename is given as - then the input gets taken from standard input. and compressed files (.gz, .Z, .bz2) are automatically uncompressed for you. she does the work, you do nothing, slay ✨

FASTA format files get 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. that's the whole vibe check.

if you wanna load -fasta files from STDIN, then 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 bulk load requires that:

• the database be on the local machine
• 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

(transiently!! like a situationship but for tables 😭)

local data may now be uploaded to a remote server via the --local option with the database host specified in the dsn, e.g. dbi:mysql:test:db_host 🌈

the adaptor used is dbi::mysqlopt. there is currently no way to change this. it is what it is, periodt 💅

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 👑

note that Windows users must use the --create option. not optional. mandatory. 💀

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. she was built for the long haul fr fr 🧚

---

👑 COMMAND-LINE OPTIONS 👑

command-line options can be abbreviated to single-letter options. e.g. -d instead of --database. cute and efficient, we love a shortcut 🎀

• --database <dsn> — Database name (default dbi:mysql:test)
• --adaptor — Adaptor name (default mysql)
• --create — Reinitialize/create data tables without asking (bold move, no questions asked 😭)
• --user — Username to log in as
• --fasta — File or directory containing fasta files to load
• --long_list — Directory containing a very large number of GFF and/or FASTA files
• --password — Password to use for authentication
  • (Does not work with Postgres, password must be supplied interactively or be left empty for ident authentication)
• --maxbin — Set the value of the maximum bin size
• --local — Flag to indicate that the data source is local
• --maxfeature — Set the value of the maximum feature size (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

---

🌈 SEE ALSO 🌈

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

like, go read those too bestie, they're part of the friend group 🫶

---

💜 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.

---

and that's the page!! 🎀✨ she's stamped perl v5.30.0, dated 2020-01-13, and filed under BP_BULK_LOAD_GFF(1p) — take care of her, mwah 💖🌸🦋