SLICE_MERCATOR_ALIGNMENT(1)

💖 SLICE_MERCATOR_ALIGNMENT 💖

okay bestie, welcome to the slice_mercator_alignment manual page — it's a User Command, it lives in section 1, and it's about to become your new hyperfixation. no cap. 🦋

✨ NAME ✨

slice_mercator_alignment — grabs the matching subalignment out of a Mercator multiple alignment. it's giving "scissors but for alignments" 💅

🌸 SYNOPSIS 🌸

slice_mercator_alignment [options] <genome> <chromosome> <start> <end>
<strand>

that's five little positional besties at the end there: <genome>, <chromosome>, <start>, <end>, <strand>. they come after your options. periodt.

🎀 DESCRIPTION 🎀

so slice_mercator_alignment ships with FSA 1.15.9 — that's the version, remember it for the vibe check. ⭐

what it does: it extracts the corresponding subalignment from a Mercator multiple alignment. literally that. you point it at a region, it pulls the matching slice of the alignment out. iconic behavior honestly.

👑 OPTIONS 👑

• -h, --help — show this message. the classic. your escape hatch. 🙈
• -D, --data <directory> — path to map, genome and alignment files. all three, one flag, main character energy.
• -M, --map <directory> — path to map and genome files.
• -A, --align <directory> — path to alignment files.
• -L, --lazy — warn, rather than die, if the subalignment can't be obtained. yes bestie, be lazy, i support you 🫶 (it warns instead of killing the whole run.)
• -U, --truncate — truncate unmappable sequence (rather than skipping) and show the truncated subalignment.
• -s, --stockholm — use and display Stockholm-format alignments with conservation statistics. the default is multi-FASTA, so this is the ✨fancy✨ mode.
• -0, --zerobased — coordinates are 0-based. the default is 1-based, so don't come at it with your zero-indexed nonsense unless you say so.
• -o, --halfopen — end coordinate is open, i.e., [start, end).

🌈 THE LORE (extra deets) 🌈

so by default it assumes coordinates are 1-based and fully-closed, which means the interval is [start, end]. fully closed. no gaps, no games.

if you asked for it (that's the -U, --truncate vibe), unmappable sequence will be truncated to the mappable portion. heads up though: the truncation will favor the beginning of the requested sequence. so the start wins. sorry to the end bestie 😭

and if the requested sequence is on the - strand, then the corresponding subalignment will be reverse-complemented. it just does that. no notes. 💜

🧚 AUTHOR 🧚

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. slay, Andreas, thank you for your service 🫡💖

and that's the whole page, bestie — sign-off time: this is slice_mercator_alignment 1.15.9, dated December 2015 🌸 go forth and slice those alignments, you gorgeous genius 💅✨