GETCOUNTS.PY(1)

💖 GETCOUNTS.PY(1) 💖

okay bestie, welcome to the User Commands section, we're doing getCounts.py today and honestly? iconic behaviour.

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✨ NAME ✨

getCounts.py — bestie this thing generates read counts for each input file. that's the whole job. that's the assignment. 💅

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🌸 SYNOPSIS 🌸

getCounts.py [options] [<inputFile.thetaMeans>]+

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🦋 DESCRIPTION 🦋

so the way this works is: this program reads the .thetaMeans files you hand it, and then — using either the info sitting in your .prob files or the Nmap option — it generates read counts for every single input file you provided. yes, every one. no cap. ✨

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💅 OPTIONS 💅

• -h, --help — shows this help message and dips. that's it, that's the whole personality. 🫶
• -o OUT, --outFile=OUT — the output file. where the goods go. 💖
• -v, --verbose — verbose output. she talks more. we love a chatty queen. 🗣️
• -p PROBDIR, --probDir=PROBDIR — the directory holding your .prob files. the program goes poking around in there looking for files with the same name but with the .prob extension instead, so it can figure out the total-aligned-read counts for each experiment. lowkey detective work. 🔍
• -n NMAP, --Nmap=NMAP — a comma separated list of total aligned-read-counts, one for each experiment. 🍓

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🌈 A cute little sign-off 🌈

this whole vibe was brought to you by getCounts.py version 0.7.5+dfsg, dated September 2021. periodt. 💜