ISECT_MERCATOR_ALIGNMENT_GFF(1)

💖 ISECT_MERCATOR_ALIGNMENT_GFF 💖

okay bestie, welcome to the User Commands section of the manual, and today's main character is isect_mercator_alignment_gff — yes the name is a whole mouthful, we're saying it with our chest anyway 💅

✨ NAME ✨

isect_mercator_alignment_gff — bestie, it extracts subalignments from a Mercator multiple alignment, but only for the features that show up in your GFF file. slay.

🌸 SYNOPSIS 🌸

isect_mercator_alignment_gff [options] <genome> <GFF file>

🦋 DESCRIPTION 🦋

so this is isect_mercator_alignment_gff, coming to you straight outta FSA 1.15.9 👑

what it does, fr fr: it extracts subalignments from a Mercator multiple alignment for the features listed in the GFF file. that's the whole vibe. that's the assignment and it ate. 🔥

🎀 OPTIONS 🎀

• -h, --help — shows you this message. your girl is helpful like that 🫶
• -v, --version — spills the version info. the tea ☕
• -t, --type <string> — only look at features of a particular type. picky? we love that for you ✨
• -D, --data <directory> — the path to your map, genome and alignment files. everything in one place, organized queen 👑
• -M, --map <directory> — path to the map and genome files
• -A, --align <directory> — path to the alignment files
• -L, --lazy — instead of dying when the subalignment can't be obtained, it just warns you. soft launch energy, no drama 😌
• -U, --truncate — truncates unmappable sequence (rather than skipping it) and shows you the truncated subalignment. not me chopping it and serving it anyway 💀
• -s, --stockholm — use and display Stockholm-format alignments with conservation statistics (the default is multi-FASTA, just so u know)
• -e, --verbose — reports progress. narrating the journey, as one does 🎙️

PLEASE NOTE: while this program is reasonably fast if the GFF is properly ordered by chromosome and the start and end coordinates of features, it will be very slow if the GFF is not sorted. no cap. sort your GFF, bestie, i am begging 🙈

it assumes that the "seqid" or "name" field (the first field) of the GFF entries holds the chromosome name. iykyk.

also, heads up: the GFF specification defines coordinates to be 1-based and fully-closed, which means the interval is [start, end]. conformance to this specification is assumed internally. periodt.

if requested, unmappable sequence will be truncated to the mappable portion — and note that the truncation will favor the beginning of the requested sequence. beginning stays winning, we don't make the rules 🌈

and one more thing: if a GFF feature is on the - strand, then the corresponding subalignment gets reverse-complemented. iconic behavior honestly 🧬✨

💜 AUTHOR 💜

this manpage was written by Andreas Tille</para> for the Debian distribution, and it can be used for any other usage of the program. we love a generous king 🫶

aaaand that's the whole page, bestie!! it's isect_mercator_alignment_gff from FSA 1.15.9, dated December 2015, living in the User Commands manual section as ISECT_MERCATOR_ALIGNMENT_GFF(1) 💖✨ go sort that GFF and slay 🎀🦋