BP_FAST...TO_TABLE(1)

📦 version 1.7.8, in nixos 26.05, nixpkgs unstable

💅 BP_FAST...TO_TABLE(1) — like, the whole manual, bestie

okay so this page lives in section 1 of the manual (that's BP_FAST...TO_TABLE(1) if you're keeping track 🎀), and it's all about fastm9_to_table — the little script that turns your FASTA -m 9 output into NCBI -m 9 tabular output. glow-up of the century tbh ✨

🌸 NAME 🌸

fastm9_to_table — turn FASTA -m 9 output into NCBI -m 9 tabular output. that's it, that's the whole vibe 🦋

✨ SYNOPSIS ✨

fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...

💖 DESCRIPTION 💖

okay first things first, the command line options, because that's what you're here for:

  • -e/--evalue evalue — filter by evalue 🔥
  • -b/--bitscore bitscore — filter by bitscore 🔥
  • --header — boolean flag to print the column header 👑
  • -o/--out — optional outputfile to write data, otherwise it will write to STDOUT 💫
  • -h/--help — show this documentation 🫶

ngl, this isn't technically a SearchIO script, because it doesn't use any Bioperl components — but it's useful and fast, which, honestly? main character energy 💅

the output is tabular output with the standard NCBI -m9 columns, and here's the lineup, in order, no cap:

queryname
hit name
percent identity
alignment length
number mismatches
number gaps
query start  (if on rev-strand start > end)
query end
hit start (if on rev-strand start > end)
hit end
evalue
bit score
🩷 bestie, note the rev-strand thing: for both query start and hit start, if it's on the rev-strand then start > end. iconic of them, honestly.

and additionally 3 more columns are provided (yes, the list has more than three entries — we're just reporting the facts here, don't come for me 😭):

fasta score
sw-score
percent similar
query length
hit length
query gaps
hit gaps

🌈 AUTHOR - Jason Stajich 🌈

Jason Stajich — jason_at_bioperl-dot-org 💌

🎀 the cute sign-off 🎀

and that's the page, babes! this beauty is perl v5.42.3, dated 2021-02-03, and it's BP_FAST...TO_TABLE(1) all day long. go forth and tabulate ✨💖🦋

📦 where this page comes from