BP_INDEX(1)

🌸 BP_INDEX 💅

okay bestie, so this one's a Perl script from the Bioperl world, living in the User Contributed Perl Documentation section of your man pages. Pull up a chair, we're doing indexes today ✨

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💖 NAME 💖

bp_index.pl — it indexes your files so that bp_fetch.pl can come along later and actually find stuff. it's giving backstage crew energy tbh 🎀

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🦋 SYNOPSIS 🦋

bp_index.pl index_name file1 file2 etc.

that's the whole vibe. a name, then a bunch of files. no cap 💅

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✨ DESCRIPTION ✨

so bp_index.pl builds a bioperl index for whatever sequence files you hand it in the argument list, and it files the whole thing under the index name you give it. think of it as making a little searchable map so future-you doesn't have to grep through a six-gig file, icon behavior fr 🫶

like, for example:

bp_index.pl nrdb /data/nrdb/nrdb.fasta

that builds an index called nrdb (that's the index name) for the file nrdb.fasta. slay. and then:

bp_index.pl -fmt EMBL swiss /data/swiss/*.dat

that one builds an index called swiss for every file in /data/swiss that ends in .dat and is in EMBL format. the shell glob does the heavy lifting, we just sit there looking cute 💅

the indexes are built on top of the Bio/Index/* modules — specifically Bio::Index::EMBL and the Bio::Index::Fasta modules. and here's the cute part: any script that uses those modules can use the index you just made. it's a whole shared ecosystem, iykyk 🌈

the iconic example script is bp_fetch, which fetches sequences and pipes them straight to STDOUT, like:

bp_fetch swiss:ROA1_HUMAN

that pulls the ROA1_HUMAN sequence out of the swiss index and writes it out as fasta format on STDOUT. obsessed 😭

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👑 OPTIONS 👑

• -fmt <format> — the format, bestie. your choices are Fasta (this is the default, no stress), swiss or EMBL.
• -dir <dir> — tells it where the index files actually live. heads up: this overrides the BIOPERL_INDEX environment variable. it's the boss now 💅

🧚 Options for expert use 🧚

• -type <db_type> — the DBM_file type. this one overrides the BIOPERL_INDEX_TYPE environment variable. only touch this if you know what you're doing, bestie 🙈
• -v — verbose mode! it reports every single index addition. this is a debugging thing, so it's gonna be a lot of output 🔥

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🍓 ENVIRONMENT 🍓

bp_index and bp_fetch coordinate where the databases actually lie using the environment variable BIOPERL_INDEX. you can override that with the -dir option if you'd rather do it inline.

⚠️ real talk: there is no default value for this one. so you must use the -dir option or set BIOPERL_INDEX yourself. otherwise it's just out here with no idea where anything is 😭

the DB type is coordinated with BIOPERL_INDEX_TYPE. and if that isn't set? it defaults to whatever the bioperl modules have installed, which itself defaults to SDBM_File. layers, babe. it's layers 🎀

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💜 USING IT YOURSELF 💜

bp_index.pl is a script that drives the Index modules — it's a wrapper, basically a cute little chauffeur for the real machinery.

so here's the advice: if you're gonna use this script heavily in your work, and your work is Perl based, it is almost certainly better to go look at the code in this script and copy it across into your own thing. and honestly? you'll probably be more likely to want the bp_fetch code instead. just saying 👀💅

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🌸 EXTENDING IT 🌸

bp_index is literally just a wrapper around James Gilbert's excellent Index modules found in bioperl. that's it. that's the whole thing. give the man his flowers 👑✨

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🎀 FEEDBACK 🎀

💌 Mailing Lists 💌

user feedback is an integral part of the evolution of this and other Bioperl modules — like genuinely, they want to hear from you 🫶 send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system — that's how they keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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⭐ AUTHOR - Ewan Birney ⭐

Ewan Birney <birney@ebi.ac.uk>

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okay that's the whole page, you ate that 💅💖 this lovely little doc is from perl v5.42.3, dated 2021-02-03, filed under User Contributed Perl Documentation — go build some indexes, bestie, and remember: set BIOPERL_INDEX 🌈✨🦋