MAKE_BED.PY(1)

💖 MAKE_BED.PY(1) 💖

okay bestie, welcome to the make_bed.py manual page — it's a User Commands situation, and I'm gonna walk you through it like we're texting at 2am. no cap, every single detail is staying in here. let's go 🦋

✨ NAME ✨

make_bed.py — find methylation in nanopore reads 🔬💅

🌸 DESCRIPTION 🌸

okay so first things first, this thing is chatty and it will absolutely yell at you before it does anything useful. expect this little gremlin of a warning to pop up:

/usr/lib/python3/dist-packages/joblib/_multiprocessing_helpers.py:53: UserWarning: [Errno 13] Permission denied.  joblib will operate in serial mode

warnings.warn('%s. joblib will operate in serial mode' % (e,))

so yeah, if joblib can't do its parallel thing it just goes serial mode and warns you about it. not a vibe, but we move. 🫶

here's how you're supposed to call it:

usage: make_bed.py [-h] [-d MIN_READ_DEPTH] [-t MOD_THRESHOLD] -f MCALLER_FILE
       [-p POSITIONS] [--control] [--gff] [--ref REF] [--plot]
       [--plotsummary] [--plotdir PLOTDIR] [--vo] [-v]

and what does it do, you ask? it produces a bed file of methylated positions based on mCaller output. literally that's the whole assignment. iconic. 👑

🎀 optional arguments 🎀

these are the little knobs and dials, bestie. every single one, no skipping:

• -h, --help — shows this help message and dips. the classic. show the help, then exit. 🙈
• -d MIN_READ_DEPTH, --min_read_depth MIN_READ_DEPTH — minimum coverage of position to determine methylation. the default is 15, so if you don't say anything it's rolling with 15. 📊
• -t MOD_THRESHOLD, --mod_threshold MOD_THRESHOLD — minimum fraction of observations with probability of methylation >=50% at a position to include in report. default is 0.5. so half-ish, that's the threshold, periodt. 🌈
• -f MCALLER_FILE, --mCaller_file MCALLER_FILE — the output file from mCaller to summarize. yeah this one's basically required, it's the whole point. 💖
• -p POSITIONS, --positions POSITIONS — a ~bed file of positions for which to calculate % of methylated reads, formatted as (chromosome,start,end,strand). heads up: this one ignores other thresholds. it does its own thing. 💅
• --control — take unmethylated positions as a control for motif detection. science! 🧚
• --gff — output PacBio-style gff instead of bed. and the "identificationQv" score will be average probability of methylation. cute little format swap. ✨
• --ref REF — use reference fasta to output longer contexts surrounding a base, from -20 to +20. zoomed in on the neighborhood. 🔍
• --plot — plot currents deviations at the positions included. > not recommended for many positions, bestie, it will simply be too much. 🫠
• --plotsummary — plot currents deviations summarized across the positions included. the chill version of the above. 📈
• --plotdir PLOTDIR — output directory for plots, default is mCaller_position_plots. 📁
• --vo — verbose output including probabilities for each position. it's giving yapper mode, but make it data. 🗣️
• -v, --version — print version. short and sweet. ⭐

and that's the whole page, bestie!! 🎀 this was make_bed.py 1.0.3+git20210331.f... from June 2021 — mwah, thanks for reading, ily, go make some beds 💖🦋👑