CNVKIT_ACCESS(1)

✨ CNVKIT_ACCESS(1) ✨

okay bestie, so you know how we're always out here doing copy-number stuff and we need to know where in the genome we can actually trust the sequence? yeah. that's this. it's cnvkit_access, living in the User Commands section of your friendly neighborhood manual, and it is here to list the locations of accessible sequence regions in a FASTA file. that's the whole vibe. 🧬✨

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🌸 NAME 🌸

cnvkit_access — list the locations of accessible sequence regions in a FASTA file.

(Yes, the real one is cnvkit.py access. The manual page just calls it cnvkit_access because man pages love a glow-up. 💅)

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🦋 DESCRIPTION 🦋

here's the usage, and no we are not paraphrasing it, this is the actual shape of the command:

usage: cnvkit.py access [-h] [-s MIN_GAP_SIZE] [-x EXCLUDE] [-o
FILENAME]

       fa_fname

ok so real talk, the way this works is: you hand it a genome FASTA, it goes through and figures out which chunks of the sequence are actually accessible (i.e. not full of N's and gaps and general chaos), and then it writes those regions out for you. it's giving "here's where the good stuff is" energy. 👑

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🎀 positional arguments: 🎀

• fa_fname — the name of your Genome FASTA file. that's the genome, bestie. the whole thing. the big one. 🧬

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💖 options: 💖

• -h, --help — show this help message and exit. the classic. the icon. when in doubt, ask it for help. 🙈
• -s MIN_GAP_SIZE, --min-gap-size MIN_GAP_SIZE — the minimum gap size between accessible sequence regions. any regions that are separated by less than this distance get joined together into one region. so basically: tiny gaps get smooshed. it's a merge, not a delete. the default is 5000. Default: 5000 ✨
• -x EXCLUDE, --exclude EXCLUDE — extra regions you want to exclude, given in BED format. and yes you can use this flag multiple times — stack those exclusions, go off. 🚫
• -o FILENAME, --output FILENAME — the name of the output file. where the accessible regions go. your little treasure map, saved to disk. 💾

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🫶 friendly reminder: the defaults are defaults for a reason. -s starts at 5000 unless you say otherwise. don't be surprised when your gaps get merged, that's literally the whole job.

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and that's the page, bestie! cnvkit.py access, version 0.9.10, dated July 2023 — documented here for you with love, glitter, and zero factual inaccuracies. now go map some accessible regions, you absolute legend. 💅🌸🦋⭐

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