PARSEVAL(1)

💖 PARSEVAL(1) 💖

okay so bestie, welcome to parseval — the manual page, but make it cute. It's a User Command, it lives in section 1 of your man pages, and it is so good at what it does. Let's get into it. 🦋

✨ NAME ✨

parseval — comparative analysis of two alternative sources of annotation

like, it literally compares two sets of annotations and tells you how they line up. main character behaviour fr.

🌸 SYNOPSIS 🌸

parseval [options] reference.gff3 prediction.gff3

💅 DESCRIPTION 💅

Okay so here's the tea. parseval takes a reference.gff3 and a prediction.gff3 and does a whole comparative analysis situation between the two. There are three little families of options and I'm gonna walk you through every single one of them, no skips. 💖

🎀 Basic options 🎀

• -d, --debug — print debugging messages. yes queen, show me everything.
• -h, --help — print the help message and exit. 🫶
• -l, --delta INT — extend gene loci by this many nucleotides; default is 0. zero, as in, no extending, as in, untouched.
• -V, --verbose — print verbose warning messages. not to be confused with the other one, bestie, look at the case!!
• -v, --version — print version number and exit. ⭐

🧚 Output options 🧚

• -a, --datashare STRING — location from which to copy shared data for HTML output (if `make install' has not yet been run). iykyk.
• -f, --outformat STRING — indicate desired output format; possible options: 'csv', 'text', or 'html' (default='text'); in 'text' or 'csv' mode, will create a single file; in 'html' mode, will create a directory. 🌈
• -g, --nogff3 — do no print GFF3 output corresponding to each comparison. (that's the original wording, and honestly? iconic. we don't fix it, we respect it.)
• -o, --outfile FILENAME — file/directory to which output will be written; default is the terminal (STDOUT). 💖
• -p, --nopng — in HTML output mode, skip generation of PNG graphics for each gene locus. no pngs, no problem.
• -s, --summary — only print summary statistics, do not print individual comparisons. just the receipts, not the whole conversation.
• -w, --overwrite — force overwrite of any existing output files. careful bestie, this one does not play.
• -x, --refrlabel STRING — optional label for reference annotations.
• -y, --predlabel STRING — optional label for prediction annotations.

🍓 Filtering options 🍓

• -k, --makefilter — create a default configuration file for filtering reported results and quit, performing no comparisons. it dips out before doing any work, respectfully.
• -r, --filterfile STRING — use the indicated configuration file to filter reported results; (yes the semicolon is part of the original, we're keeping it, periodt)
• -t, --maxtrans INT — maximum transcripts allowed per locus; use 0 to disable limit; default is 32. ⭐

reminder bestie: the flags are case sensitive — -V is verbose warnings and -v is the version number. Do not mix them up or you will be confused and I will be sad. 😭

and that's the whole page, you ate that. 💅✨🦋

This one's parseval version 0.15.1, dated January 2016, straight from the User Commands corner of your friendly neighbourhood man pages. bye bestie, go compare some annotations 💖