BP_SEQRET(1)

📦 version 1.7.8, in nixos 26.05, nixpkgs unstable

🌸 NAME 🌸

okay so, this is BP_SEQRET(1), from User Contributed Perl Documentation — section 1, bestie. It's the page for bp_seqret: a bioperl implementation of sequence fetch from local db (like EMBOSS seqret). slay. 💅

✨ USAGE ✨

The whole bp_seqret situation, synopsis-style:

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

🎀 flag lineup 🎀

  • -f, --format — this is where outputformat goes.
  • -o, --out, --outfile — this is where outfile goes.
  • -d, --db — this is where dbname goes.
  • -i, --id, -s, --seqname — this is where seqname1 goes.

🌈 example usage 🌈

The examples, verbatim, because we do not mess with commands:

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. Periodt. ✨

Output format is Fasta by default — no cap. 🦋

If no output filename is provided then output is written to STDOUT. Providing '-' as the output filename will accomplish the same thing. iykyk 💖

💖 AUTHOR 💖

Jason Stajich jason_AT_bioperl-dot-org 🫶

mwah 💋 final vibe check: this page is from perl v5.42.3, dated 2021-02-03 — catch you in the group chat! 💖✨🎀

📦 where this page comes from