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David Pattinson davipatti

  • UW-Madison
  • New York, USA
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#!/usr/bin/env python3
"""
Set a sleep timer on a Sonos speaker.
Example:
$ python sonos-sleep.py --name Bathroom --minutes 20
"""
import argparse
@davipatti
davipatti / test.pdb
Created August 14, 2020 21:24
Naught pdb file
This file has been truncated, but you can view the full file.
ATOM 1 MN1 GLN A 44 43.240 91.770 46.070 1.00 0.00
ATOM 2 MN2 GLN A 44 43.780 92.310 45.780 1.00 0.00
ATOM 3 N GLN A 44 43.490 92.030 45.870 1.00 0.00 N
ATOM 4 H1 GLN A 44 42.960 91.470 46.520 1.00 0.00 H
ATOM 5 H2 GLN A 44 44.480 91.830 45.970 1.00 0.00 H
ATOM 6 H3 GLN A 44 43.340 93.010 46.060 1.00 0.00 H
ATOM 7 CA GLN A 44 43.070 91.710 44.490 1.00 0.00 C
ATOM 8 HA GLN A 44 41.970 91.720 44.520 1.00 0.00 H
ATOM 9 CB GLN A 44 43.480 92.850 43.500 1.00 0.00 C
ATOM 10 HB1 GLN A 44 42.840 93.720 43.700 1.00 0.00 H
@davipatti
davipatti / svg-to-np-array.py
Created August 12, 2020 14:30
Extract xy coordinates from svg
#!/usr/bin/env python
# Extracting xy coordinates from an svg path using svgpathtools
# https://github.com/mathandy/svgpathtools
# pip install svgpathtools
from svgpathtools import parse_path
import numpy as np
path = "M 125.09006,141.18848 C 110.99811,164.35846 111.22868,108.07854 83.831725,113.54159 56.434773,119.00464 91.156393,169.4818 61.713214,168.35114 32.270035,167.22048 81.822001,142.5491 60.875654,122.49307 39.929306,102.43705 13.745665,149.24722 6.4082722,121.25037 -0.92912038,93.253532 42.338807,123.59851 43.351984,95.418206 44.365161,67.2379 -6.2345334,65.117335 11.759409,43.777931 29.753351,22.438526 42.683955,75.303807 69.420586,63.044694 96.157218,50.78558 64.480031,7.6180619 90.699813,14.891972 c 26.219787,7.27391 -22.120071,45.96694 0.83756,61.421875 22.957637,15.454936 45.837447,-38.115775 52.856287,-9.974186 7.01884,28.141589 -35.94694,7.378485 -41.50034,35.827669 -5.553398,28.44918 36.28869,15.85118 22.19674,39.02115 z"
@davipatti
davipatti / jupyter-nb-pelican-fields.txt
Created July 13, 2020 16:08
Jupyter notebook pelican fields
- title:
- date:
- summary:
- author:
- category:
@davipatti
davipatti / stdout
Created June 5, 2020 20:02
raxml-ng re-generating parsimony starting tree
RAxML-NG v. 0.9.0git released on 26.11.2019 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
RAxML-NG was called at 02-Jun-2020 09:39:21 as follows:
./raxml-ng --tree pars{1} --msa b-nuc.translated.sort.hd1.curated.fasta --prefix FLU --model FLU+F+I --log VERBOSE --threads 8
@davipatti
davipatti / ali.fasta
Created June 2, 2020 13:36
Influenza B HA amino acid sequences which are causing raxml-ng to crash
This file has been truncated, but you can view the full file.
>B/PENNSYLVANIA/1/2007_h207B7D2B#2007-02-26#
DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSYFANLKGTRTRGKLCPDCLNCTDLDVALGRPMCVGTTPSAKASILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSTQNVIDAEKAPGGPYRLGTSGSCPNATSKSGFFATMAWAVPK-DNNKNATNPQTVEVPYICTEGEDQITVWGFHSDNKIQMKNLYGDSNPQKFTSSANGVTTHYVSQIGGFPDQTEDGGLPQSGRIVVDYMMQKPGKTGTIVYQRGVLLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLKERGFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVDIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDSLNITAASLNDDGLDNHTILLYYSTAASSLAVTLMLAIFIVYMVSKDNVSCSICL
>B/PENNSYLVANIA/1/2007_h095F9CB8#2007-02-26#
DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSYFANLKGTRTRGKLCPDCLNCTDLDVALGRPMCVGTTPSAKASILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSTQNVIDAEKAPGGPYRLGTSGSCPNATSKSGFFATMAWAVPK-DNNKNATNPQTVEVPYICTEGEDQITVWGFHSDKKTQMKNLYGDSNPQKFTSSANGVTTHYVSQIGGFPDQTEDGGLPQSGRIVVDYMMQKPGKTGTIVYQRGVLLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLKERGFFGAIAGFLEGGWEG
@davipatti
davipatti / stdout
Created April 27, 2020 22:10
lc0 build fail - not loading cublas_v2
david@puck~/D/lc0> ./build.sh
~/Downloads/lc0 ~/Downloads/lc0
[0/1] Regenerating build files.
The Meson build system
Version: 0.51.2
Source dir: /home/david/Downloads/lc0
Build dir: /home/david/Downloads/lc0/build/release
Build type: native build
Project name: lc0
Project version: undefined
@davipatti
davipatti / stdout
Created April 27, 2020 21:53
lc0 build fail
david@puck~/D/lc0> ./build.sh
~/Downloads/lc0 ~/Downloads/lc0
[0/1] Regenerating build files.
The Meson build system
Version: 0.51.2
Source dir: /home/david/Downloads/lc0
Build dir: /home/david/Downloads/lc0/build/release
Build type: native build
Project name: lc0
Project version: undefined
@davipatti
davipatti / stdout
Created April 27, 2020 20:28
lc0 build fail
david@puck~/D/lc0> ./build.sh
~/Downloads/lc0 ~/Downloads/lc0
[0/1] Regenerating build files.
The Meson build system
Version: 0.51.2
Source dir: /home/david/Downloads/lc0
Build dir: /home/david/Downloads/lc0/build/release
Build type: native build
Project name: lc0
Project version: undefined
@davipatti
davipatti / stderr
Created April 27, 2020 20:24
lc0 build fail
david@puck~/D/lc0> ./build.sh
~/Downloads/lc0 ~/Downloads/lc0
The Meson build system
Version: 0.51.2
Source dir: /home/david/Downloads/lc0
Build dir: /home/david/Downloads/lc0/build/release
Build type: native build
Project name: lc0
Project version: undefined
C++ compiler for the host machine: ccache c++ (gcc 9.2.1 "c++ (Ubuntu 9.2.1-9ubuntu2) 9.2.1 20191008")