MAP_COORDS(1)

💖 map_coords — the manual, but make it make sense 💖

okay bestie, so this is map_coords(1), a User Commands page, and it comes to you straight from the FSA 1.15.9 era (December 2015 energy, but the knowledge is timeless fr fr). it's here to help you translate coordinates from one genome to another, and it does it using a Mercator multiple alignment. slay. let's get into it 💅

✨ NAME ✨

map_coords — Map coordinates from one genome to another using a Mercator multiple alignment

like. that's the whole vibe. you've got coordinates. they live in one genome. you want them to live in another one. this is the tool that does the glow-up ✨

🦋 SYNOPSIS 🦋

map_coords [options] <source genome> <chromosome> <start> <end> <strand>
<target genome>

notice the shape of it, bestie: <source genome>, then <chromosome>, then <start>, <end>, <strand>, and finally <target genome>. six positional arguments, in that exact order, no cap. [options] go up front. 👑

🌸 DESCRIPTION 🌸

map_coords is from FSA 1.15.9 and its whole main character job is this: Map coordinates from one genome to another using a Mercator multiple alignment.

that's it, that's the mission statement. you hand it coordinates in your source genome, and it finds where those same coordinates land in your target genome, using a Mercator multiple alignment to do the actual translation. it's giving molecular cartography 🗺️✨

🎀 OPTIONS 🎀

• -h, --help — show this message. your girl -h is always there when you need her, no judgment, no questions asked 🫶
• -D, --data <directory> — path to map, genome and alignment files. the everything-bagel option: maps, genomes AND alignments, all in one directory 🍓
• -M, --map <directory> — path to map and genome files. just the maps and the genomes, hold the alignments 💜
• -A, --align <directory> — path to alignment files. only the alignment files, nothing else, keep it minimal ✨
• -L, --lazy — warn, rather than die, if the subalignment can't be obtained. she's not dramatic, she's chill. instead of 💀ing the whole run, she just warns you and keeps it moving 😌
• -U, --truncate — truncate unmappable sequence (rather than skipping) and show truncated subalignment. so instead of skipping over the unmappable bit, she trims it and shows you the truncated subalignment 🌈

🧚 A LITTLE HEADS-UP ABOUT COORDINATES 🧚

Assumes that coordinates are <strong>1-based</strong> and <strong>fully-closed</strong>, therefore representing the interval <code>[start, end]</code>.

read that twice, bestie. 1-based. fully-closed. so your <start> and your <end> are BOTH included in the interval, giving you the range [start, end] 🎯

not me forgetting that fully-closed means both endpoints count... anyway. don't be like me. 🙈

If requested, unmappable sequence will be truncated to the mappable portion; note that the truncation will favor the beginning of the requested sequence. so when the trimming happens, the front of your sequence is the one getting priority — the beginning stays, the tail is what gets cut ✂️

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you Andreas, you ate 💖

and that's the whole page, bestie. this was map_coords version 1.15.9, dated December 2015 — go map some coordinates, you've got this. periodt. 💅✨🦋