MAP_GFF_COORDS(1)

💖 MAP_GFF_COORDS — the bestie guide 💖

okay so hi!! welcome to map_gff_coords(1), a lil section-1 user command that's about to become your new obsession 🦋 this is the manual page for the map_gff_coords program, and I'm gonna walk you through literally every single thing it does, no skips, no shortcuts, periodt.

✨ NAME ✨

map_gff_coords — maps the coordinates of GFF features from one genome over to another one, using a Mercator multiple alignment. it's giving genome glow-up 💅

🌸 SYNOPSIS 🌸

map_gff_coords [options] <source genome> <source GFF file> <target genome>

that's it bestie, three lil positional args and a pile of options 👑

🎀 DESCRIPTION 🎀

so this is map_gff_coords from FSA 1.15.9 — yes, that's the version, write it down 🖊️

what it does: it takes the coordinates of GFF features and maps them from one genome onto another, using a Mercator multiple alignment as the bridge. like a coordinate translator but for genomes, no cap ✨

💜 OPTIONS 💜

• -h, --help — shows you this message. your emotional support flag fr fr 🫶
• -t, --type <string> — only look at features of a particular type. filter queen behavior 👑
• -D, --data <directory> — the path to the map, genome and alignment files. one directory to hold them all 🎀
• -M, --map <directory> — the path to the map and genome files 🗺️
• -A, --align <directory> — the path to the alignment files 🌈
• -L, --lazy — warn instead of straight-up dying if the subalignment can't be obtained. gentle parenting mode 😌
• -U, --truncate — truncate the unmappable sequence instead of skipping it, and show the truncated subalignment. cutting it off, not ghosting it ✂️
• -f, --force-entry — if a feature can't be mapped, add an empty entry to the GFF file instead of skipping it entirely. also, heads up: this one implies --lazy 💀
• -e, --verbose — reports progress. because bestie deserves to know what's happening 💖

PLEASE NOTE: while this program is reasonably fast if the GFF is properly ordered by chromosome and by the start and end coordinates of features, it will be very slow if the GFF is not sorted. like, go-get-a-snack slow 😭 it also assumes that the "seqid" or "name" field — the first field of the GFF entries — holds the chromosome name.

also important: the GFF specification defines coordinates as 1-based and fully-closed, which means they represent the interval [start, end]. this program assumes conformance to that spec internally, so don't come at it with anything else 🙈

if you request it, unmappable sequence will be truncated to the mappable portion — and note that the truncation will favor the beginning of the requested sequence 🧚

and one more thing, this one's iconic: if a GFF feature is on the + strand for the source genome, but the corresponding homologous region in the target genome is on the - strand, then the mapped GFF feature will be reported as being on the - strand. plot twist, but make it scientific 🔥

⭐ AUTHOR ⭐

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program 💫

and that's the whole page bestie, you ate it 🍓

signing off: map_gff_coords 1.15.9, from December 2015 — manual page MAP_GFF_COORDS(1) 💜 bye ily, go map some coords