BP_SEQF...RE_LOAD(1p)

💖 BP_SEQF...RE_LOAD 💖

okay bestie, gather round, because this is bp_seqfeature_load.pl and she is literally the plug for getting your GFF and fasta files into a SeqFeature database. perl v5.40.0 energy, User Contributed Perl Documentation vibes, no cap. 🫶

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✨ NAME ✨

bp_seqfeature_load.pl — Load GFF into a SeqFeature database

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🌸 DESCRIPTION 🌸

So here's the tea 🍓: you can pass any number of GFF or fasta format files (or GFF with embedded fasta, she's flexible like that) and this script will load the features and sequences into a SeqFeature database. Slay.

The database (and the adaptor) you wanna use? You specify that on the command line. And if you need a brand new SeqFeature database, just hit the --create flag. Iconic. 👑

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🦋 SYNOPSIS 🦋

bp_seqfeature_load.pl [options] gff_or_fasta_file1 [gff_or_fasta_file2 [...]]

And fr fr, if you get lost, try:

bp_seqfeature_load.pl --help

or

bp_seqfeature_load.pl --man

for more info. 💅

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👑 OPTIONS 👑

• -d, --dsn — the DBI data source (default dbi:mysql:test)
• -n, --namespace — the table prefix to use (default undef). This lets several independent sequence feature databases live inside a single database. Sharing is caring. 💜
• -s, --seqfeature — the type of SeqFeature to create... RTSC (default Bio::DB::SeqFeature)
• -a, --adaptor — the storage adaptor (class) to use (default DBI::mysql)
• -v, --verbose — turn on verbose progress reporting (default true). If you want it quiet, use --noverbose to switch this off. 🔇
• -f, --fast — activate fast loading. (default 0) Heads up, this is only available for some adaptors. 🏎️
• -T, --temporary-directory — specify temporary directory for fast loading (default File::Spec->tmpdir())
• -i, --ignore-seqregion — if true, then ignore ##sequence-region directives in the GFF3 file (default, create a feature for each region)
• -c, --create — create the database and reinitialize it (default false). > Note, this will erase previous database contents, if any. 😭 She's not playing around.
• -u, --user — user to connect to database as
• -p, --password — password to use to connect to database
• -z, --zip — compress database tables to save space (default false)
• -S, --subfeatures — turn on indexing of subfeatures (default true). Use --nosubfeatures to switch this off.
• --fts — index the attribute table for full-text search (default false). Applicable only when --create is specified. Currently applicable to the DBI::SQLite storage adaptor only (using the most recent supported FTS indexing method, which may not be portable to older DBI::SQLite versions). 🧚
• --summary — generate summary statistics for coverage graphs (default false). You can run this on a previously loaded database or during the load. It will default to true if --create is used.
• -N, --nosummary — do not generate summary statistics, to save some space and load time (default if --create is not specified; use this option to explicitly turn off summary statistics when --create is specified)
• --noalias-target — don't create an Alias attribute whose value is the target_id in a Target attribute (if the feature contains a Target attribute, the default is to create an Alias attribute whose value is the target_id in the Target attribute)

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🌈 THE GFF3 DEETS 🌈

Please see http://www.sequenceontology.org/gff3.shtml for information about the GFF3 format. BioPerl extends the format slightly by adding a ##index-subfeatures directive. Set this to a true value if you wish the database to be able to retrieve a feature's individual parts (such as the exons of a transcript) independently of the top level feature:

##index-subfeatures 1

It is also possible to control the indexing of subfeatures on a case-by-case basis by adding "index=1" or "index=0" to the feature's attribute list. This should only be used for subfeatures. ⚠️

Subfeature indexing is true by default. Set to false (0) to save lots of database space and speed performance. You may use --nosubfeatures to force this. 🔥

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and that's the whole page, bestie — every flag, every default, every warning, all present and accounted for, periodt 💅

cute lil sign-off: this one's from perl v5.40.0, dated 2024-10-11, and it's the User Contributed Perl Documentation version of BP_SEQF...RE_LOAD(1p). mwah 🎀