SEARCH_OVERVIEW(1p)

📦
version 2.40 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💅 SEARCH_OVERVIEW — no cap, it's giving graphics 💅

bestie, welcome to SEARCH_OVERVIEW(1p) from the User Contributed Perl Documentation — yes that's the whole manual name, we're being ✨official✨ today.

🌸 NAME 🌸

search_overview — Render a SearchIO parser report into a simple overview graphic

🦋 SYNOPSIS 🦋

search_overview -i filename [-f format] [-o outputfilename] [--labels]

🎀 DESCRIPTION 🎀

okay so here's the vibe: this script takes any Bio::SearchIO-parseable report and turns it into a cute lil overview graphic of that report. literally any of them. For our purposes we're assuming BLAST and the BLAST scores when assigning colors, just so you know where the color math is coming from. Output is a PNG format file. periodt.

ngl this is not meant to be an overly customized script — it's more of a quick and dirty look at a report, or a starting point for more complicated implementations. main character energy, but make it minimal. 💅

The color is determined by the hit score, which is currently pegged to the NCBI scheme and looks like this:

  • RED — >= 200
  • PURPLE — 80-200
  • GREEN — 50-80
  • BLUE — 40-50
  • BLACK — < 40

✨ OPTIONS ✨

  • -i/--input — the input filename, otherwise input is assumed from STDIN. 🫶
  • -o/--output — the output filename. this one is optional! if you do not provide the output filename, the script will create a file using the name of the query sequence and will process all the sequences in the file. but if an output filename IS provided, the script will only display an image for the first one. (yes, that's the whole trade-off, iykyk.)
  • -f/--format — the SearchIO format parser to use. if not provided, SearchIO will guess based on the file extension. she's intuitive like that. 🧚
  • -l/--labels — display the hit sequence name as a label in the overview. for lots of sequences this will make the image very long 😭 so by default it is turned off.

👑 AUTHOR 👑

Jason Stajich

Jason Stajich, jason[-at-]open-bio[-dot-]org.

ok and that's the whole page bestie, we ate and left no crumbs 💖 this was perl v5.30.0 from 2019-11-25 — go forth and render those reports, mwah 💋
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