IPIG(1)

💖 IPIG(1) 💖

okay bestie, welcome to the ipig manual page — that's the User Commands section, one (1) of the classic Unix man volumes, and yes she's a real one. sit down, grab a strawberry 🍓, we're doing genomics.

✨ NAME ✨

ipig — Integrating PSMs Into Genome browser visualizations 🧬✨

🌸 SYNOPSIS 🌸

ipig <psm file> |-g|-c|-cg [<config file>]

🦋 DESCRIPTION 🦋

so like, iPiG is obsessed with one job and one job only: taking peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications and yeeting them into genomic visualisations — the kind of genome browser visuals you get from, say, the UCSC genome browser (http://genome.ucsc.edu/). no cap, that's the whole vibe. 👑

iPiG takes your PSMs from the MS standard format mzIdentML (*.mzid) or from text format, and hands you back results in genome track formats (BED and GFF3 files), which you can just... drop into genome browsers. it's giving effortless. 💅

🎀 OPTIONS 🎀

• <psm file> — the file with your peptide spectrum matches, so mzid or txt. this is literally the thing you're feeding her. 🍽️
• -g, -gui — starts the graphical user interface of iPiG ✨ (mouse girlies rise up)
• -c, -control — starts the gene control; the necessary files have to be indicated in the configuration file, so don't come empty-handed bestie
• -cg, -controlgui — starts the graphical user interface of the gene control 🌈 (yes, control AND gui, she contains multitudes)
• -d, -downloader — starts the download gui ⬇️💖
• <config file> — you can point her at a different configuration file if you want (otherwise ipig.conf is loaded by default — that's the main character, she's always there for you)

additional requirements 🫶

• if you're using a non-gui mode, a config file (ipig.conf by default) has to contain several additional parameters, e.g. indicating the reference genome etc. 📚 — yes, "etc.", the manpage is being mysterious, we respect the mystery
• in a gui mode (-g and -cg), additional parameters can be indicated two ways: within the interface, or with a config file as well. both? both. iconic. 🙈
• have a look into readme.txt and ipig.conf for examples and more details about the additional parameters 👀 — genuinely, go look, they're the lore

💀 real talk: in non-gui mode you must have that config file with the extra parameters or nothing's happening. it is not optional and it is not a suggestion, periodt.

okay that's the whole page, mwah 💋 — this lil manual came to you from ipig 2012-06-19 and was dated February 2014, which honestly is vintage of her. stan a legacy tool. go integrate those PSMs, bestie, you're gonna slay 🧚✨💜