BP_BIOFLAT_INDEX(1)

NAME 💖

okay so welcome to BP_BIOFLAT_INDEX(1), from the User Contributed Perl Documentation — the main character here is bp_bioflat_index.pl, and it indexes sequence files using Bio::DB::Flat. slay. ✨

DESCRIPTION 🦋

bestie, this script creates or updates a biological sequence database indexed with the Bio::DB::Flat indexing scheme. The arguments are a list of flat files containing the sequence information to be indexed — literally just hand it the files and let it cook. 🔥

USAGE 🎀

run it like this, no cap:

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

Options 💅

• --create — create or reinitialize the index. If not specified, the index must already exist — like, it has to be there already, bestie. 👀
• --format <format> — the format of the sequence files. Must be one of "genbank", "swissprot", "embl" or "fasta". those are the only options, periodt.
• --location <path> — path to the directory in which the index files are stored. tell it where the index lives 🏠
• --dbname <name> — the symbolic name of the database to be created. name the baby database ✨
• --indextype <type> — type of index to create. Either "bdb" or "flat". And heads up: "binarysearch" is the same as "flat" — lowkey an alias situation.

Options can be abbreviated. For example, use -i for --indextype. iykyk 😌

Environment-variable defaults 🌈

The following environment variables will be used as defaults if the corresponding options are not provided:

• 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

mwah 💋 this page is from perl v5.42.3, dated 2021-02-03, and it's the BP_BIOFLAT_INDEX(1) manual page — catch u later, bestie! 🫶