BP_BIOFLAT_INDEX(1p)

👑 NAME 👑

bp_bioflat_index.pl — bestie, this is the lil script that indexes your sequence files using Bio::DB::Flat. 💅

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✨ DESCRIPTION ✨

okay so picture this: you've got a pile of flat files full of sequence info, and you want them in a proper biological sequence database that's indexed with the Bio::DB::Flat indexing scheme. That's literally the whole job. 🌸

You can create a fresh one or update one that already exists — your call. And the arguments? Just a list of flat files holding the sequence information you want indexed. Hand them over, one after another. Easy. 🫶

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🎀 USAGE 🎀

bp_bioflat_index.pl <options> file1 file2 file3...

Options:

• --create — create the index from scratch, or reinitialize it. ✨ If you don't pass this, the index has to already exist — no cap, it will not conjure one out of thin air.
• --format <format> — the format of your sequence files. It must be one of "genbank", "swissprot", "embl" or "fasta". That's the whole menu, bestie. 🍓
• --location <path> — the path to the directory where the index files live. 🎀
• --dbname <name> — the symbolic name of the database you're creating. 💖
• --indextype <type> — the type of index to create. Either "bdb" or "flat". And heads up: "binarysearch" is the same thing as "flat". 🔥

Fun fact: options can be abbreviated! So like, -i totally works for --indextype. Iconic behavior honestly.

And if you don't bother providing some of these options, these environment variables step in as the defaults, like the supportive besties they are: 🌈

• OBDA_FORMAT — format of sequence file
• OBDA_LOCATION — path to directory in which index files are stored
• OBDA_DBNAME — name of database
• OBDA_INDEX — type of index to create

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okay that's the whole page, mwah 💋 — this was BP_BIOFLAT_INDEX(1p), part of the User Contributed Perl Documentation, running on perl v5.32.1, dated 2021-08-15. go index something gorgeous, bestie 👑✨