PXLOG(1)

💖 PXLOG — the manual page, but make it cute 💖

okay bestie, welcome to pxlog, section 1 of the user commands manual. she's a little MCMC log file manipulator and she devours. let's get into it 🦋

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✨ NAME ✨

pxlog — MCMC log file manipulator 🧚

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✨ SYNOPSIS ✨

pxlog [OPTIONS]...

that's it. that's the whole vibe. options go in, magic comes out 💅

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✨ DESCRIPTION ✨

okay so pxlog is your MCMC log file manipulator, and she is so versatile. she can combine and resample parameters or trees across files. no cap.

and here's the thing that's genuinely iconic: the log files do not need to contain the same number of samples. she does not care. she is unbothered. 👑

input files can be indicated using wildcards, like for example '*.trees' — yes bestie, the shell does the heavy lifting for you.

parameter log files are expected to be whitespace delimited, so if you've got commas or tabs pretending to be spaces, that's a you problem.

NOTE — and this is the one everyone gets wrong: all values are in terms of number of SAMPLES, NOT generations. samples. not generations. say it with me. samples. 🫶

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✨ OPTIONS ✨

• -p, --parmf=FILE — input parameter log file(s). plural. she can take more than one 💖
• -t, --treef=FILE — input tree log file(s). also plural, also slaying 🌸
• -b, --burnin=INT — number of samples to exclude at the beginning of a file. throw the first few away, they're just warmup 🎀
• -n, --thin=INT — interval of resampling. every n-th sample gets to come to the party ✨
• -i, --info — calculate log file attributes and exit. just info, then she's out the door 🚪
• -s, --summarize — summary statistics of samples (parameter logs only, so don't try it on trees bestie)
• -c, --columns — print out column names (parameter logs only)
• -d, --delete=CSL — delete parm columns by 1-index sep by commas (NO SPACES!) ⚠️ like actually no spaces, she will not forgive you
• -k, --keep=CSL — keep only parm columns by 1-index sep by commas (NO SPACES!) ⚠️ same rule, same energy
• -v, --verbose — make the output more verbose. she will tell you everything. she will not stop 💀
• -o, --outf=FILE — output file, STOUT otherwise (yes, STOUT, that's literally what the man page says, don't come for me 🙈)
• -h, --help — display this help and exit. always a valid move 🌈
• -V, --version — display version and exit. vibe check the build 👑
• -C, --citation — display phyx citation and exit. cite your tools, it's the law of academia ⭐

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✨ CITATION ✨

if you use this, you gotta cite it, that's just manners bestie 🫶

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

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✨ AUTHOR ✨

Written by Joseph W. Brown 👑

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✨ REPORTING BUGS ✨

found a bug? not me manifesting that for you, but like, if it happens:

Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>

phyx home page: <https://github.com/FePhyFoFum/phyx>

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✨ COPYRIGHT ✨

Copyright © 2016-2024 FePhyFoFum License GPLv3

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and that's the whole page, bestie. pxlog 1.3.1, June 2024 — she's been serving since 2016 and she's still that girl. go manipulate some logs 💅💖✨