BP_SEQRET(1p)

💖 NAME 💖

okay bestie, so bp_seqret is the bioperl glow-up of sequence fetch from a local db — think EMBOSS seqret energy but make it Perl. it literally pulls sequences out of a local database file and hands them to you in whatever format you want. no cap. 🧚✨

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🌸 USAGE 🌸

the vibe check on the flags:

• -f, --format outputformat — sets the output format, bestie. pick your fave.
• -o, --out, --outfile outfile — where the output goes. yes, -o and --out and --outfile all do the same thing, it's giving generous. 🫶
• -d, --db dbname — the database you're pulling from. your local sequence stash. 💅
• -i, --id, -s, --seqname seqname1 — the name of the sequence you want. and the way you can just say it again and again for more sequences?? iconic. 🔥

the full synopsis, verbatim, no edits:

bp_seqret [-f/--format outputformat] [-o/--out/--outfile outfile]
[-d/--db dbname] [-i/--id/-s/--seqname seqname1]

✨ examples, bestie ✨

these are literally copy-pasteable, i would never lie to you:

bp_seqret -f fasta -db db.fa -i seq1 -i seq2 > output.fas
bp_seqret db.fa:seq1 output.fas
bp_seqret db.fa:seq1 -o output.fas
bp_seqret -db db.fa -o output.fas seq1 seq2 seq3
bp_seqret -db db.fa seq1 seq2 seq3 output.fas
bp_seqret -db db.fa seq1 seq2 seq3 - > output.fas

🦋 the deets 🦋

the DB is expected to be a Fasta formatted sequence file with multiple sequences. like, that's the whole thing. multiple sequences, fasta, boom. 🌈

output format is Fasta by default — so if you don't specify, that's what you're getting, periodt.

if you don't give it an output filename, the output goes straight to STDOUT. and if you pass - as the output filename? same thing, bestie — - means STDOUT. both roads lead to the terminal. 😌

ngl, - as an output filename is lowkey the same as saying nothing at all. it's the "idk just show me" option. 💀

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👑 AUTHOR 👑

this absolute legend wrote it: Jason Stajich — jason_AT_bioperl-dot-org 🎀

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that's the whole page bestie, we ate and left no crumbs 💅✨ this was perl v5.32.1, dated 2021-08-15, and it's BP_SEQRET(1p) — ily, go fetch some sequences 🦋💖