Rasmus Fonseca RasmusFonseca
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| import numpy as np | |
| from collections import defaultdict | |
| from typing import List, Tuple | |
| from math import sqrt, pow | |
| I = 1000 # Infinity |
RasmusFonseca
/ flareplot-main.js
Created
May 9, 2019 06:31
Flareplot main script with tracks moved toward center
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| /** | |
| * Creates a flareplot svg in the container matched by the `containerSelector`, sets its width to `width` pixels, | |
| * and associates it with the contents of `json` | |
| * @param width | |
| * @param inputGraph | |
| * @param containerSelector | |
| * @returns {{getNumFrames, setFrame, framesIntersect, framesSum, setTrack, setTree, getTreeNames, getTrackNames, addNodeToggleListener, addNodeHoverListener, addEdgeToggleListener, addEdgeHoverListener, graph}} | |
| */ | |
| function createFlareplot(width, inputGraph, containerSelector){ |
RasmusFonseca
/ sysusg.py
Last active
July 2, 2018 20:16
Monitor CPU-time and max memory usage using ps
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| """ | |
| Monitors a process using the `ps` command and records total CPU-time and maximum memory usage. | |
| Example usage: | |
| ./runMyCommand & | |
| sysusg.py runMyCommand | |
| """ | |
| import subprocess | |
| import sys | |
| import time |
RasmusFonseca
/ multiproducer-consumer.py
Last active
September 30, 2024 07:17
Python multiple producer / single consumer example
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| from multiprocessing import Process, Queue | |
| def square_producer(inputqueue, resultqueue): | |
| """ | |
| A producer that pops numbers off the inputqueue, squares them and puts the result on resultqueue | |
| """ | |
| while True: | |
| num = inputqueue.get() | |
| if num is None: |
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| <!DOCTYPE html> | |
| <html lang="en"> | |
| <head> | |
| <meta charset="UTF-8" /> | |
| <title>Document</title> | |
| <style> | |
| * { | |
| box-sizing: border-box; | |
| } | |
| td, th{ |
RasmusFonseca
/ flareplot-selectors1.js
Created
April 20, 2017 05:05
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| /** | |
| * Creates a tree and track selector for `flareplot` within `container`. | |
| * | |
| * If there are more than one tree in the graph a div will be added containing | |
| * radio buttons to switch between them. If the graph has more than one track | |
| * they'll be added in a div after. If there is only one tree and one track the | |
| * container will be left untouched. The resulting layout will look as follows: | |
| * <code> | |
| * <div id="container"> |
RasmusFonseca
/ momentconfig.json
Created
January 9, 2017 23:12
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| { | |
| "embeddings": [ | |
| { | |
| "tensorName": "My tensor", | |
| "tensorShape": [ | |
| 1000, | |
| 50 | |
| ], | |
| "tensorPath": "https://gist.githubusercontent.com/RasmusFonseca/b4ca7261eab30d65b3376d2af2ca46ed/raw/610b1e1ef87464769277888f192f7eb60e6dabb3/allmoments.tsv", | |
| "metadataPath": "https://gist.githubusercontent.com/RasmusFonseca/726d1b5508ec47c10d90641d71e3c7f2/raw/75788561e40b4ade4fc6981223b252cb545dbaa0/momentmetadata.tsv" |
RasmusFonseca
/ momentmetadata.tsv
Created
January 9, 2017 23:11
We can make this file beautiful and searchable if this error is corrected: No tabs found in this TSV file in line 0.
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| 100D | |
| 101D | |
| 102D | |
| 103D | |
| 104D | |
| 109D | |
| 10MH | |
| 111D | |
| 112D | |
| 113D |
RasmusFonseca
/ allmoments.tsv
Created
January 9, 2017 23:10
We can make this file beautiful and searchable if this error is corrected: It looks like row 5 should actually have 30 columns, instead of 27 in line 4.
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| 1.0000 1.3360 1.5382 1.6889 1.8106 1.9127 2.0003 2.0765 2.1437 2.2033 2.2568 2.3049 2.3486 2.3885 2.4249 2.4585 2.4895 2.5181 2.5448 2.5697 2.5929 2.6147 2.6352 2.6544 2.6726 2.6898 2.7061 2.7215 2.7362 2.7501 | |
| 1.0000 1.3915 1.6346 1.8079 1.9395 2.0436 2.1287 2.2000 2.2611 2.3142 2.3612 2.4032 2.4412 2.4758 2.5076 2.5371 2.5645 2.5901 2.6142 2.6369 2.6584 2.6787 2.6979 2.7163 2.7337 2.7503 2.7661 2.7812 2.7956 2.8094 | |
| 1.0000 1.3886 1.6307 1.8047 1.9379 2.0441 2.1312 2.2042 2.2667 2.3208 2.3683 2.4106 2.4485 2.4827 2.5140 2.5427 2.5693 2.5940 2.6171 2.6388 2.6593 2.6787 2.6971 2.7147 2.7314 2.7475 2.7628 2.7775 2.7917 2.8053 | |
| 1.0000 1.4091 1.6618 1.8415 1.9783 2.0868 2.1758 2.2504 2.3143 2.3697 2.4186 2.4621 2.5012 2.5367 2.5692 2.5990 2.6266 2.6524 2.6764 2.6989 2.7201 2.7402 2.7591 2.7772 2.7943 2.8106 2.8261 2.8410 2.8552 2.8688 | |
| 1.0000 1.3511 1.5648 1.7225 1.8484 1.9535 2.0435 2.1219 2.1910 2.2523 2.3071 2.3564 2.4008 2.4411 2.4778 2.5113 2.5421 2.5705 2.5966 2.6209 2.6435 2.6645 2.6841 2.7025 2.7198 2.7360 2. |
RasmusFonseca
/ extractFeatures.py
Created
January 2, 2017 21:38
Extracting protein features as .tsv using blosum62 from a fasta file
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| import numpy as np | |
| import sys | |
| # Amino acid substitution matrix | |
| blosum62 ={ | |
| "C":[9,-1,-1,-3,0,-3,-3,-3,-4,-3,-3,-3,-3,-1,-1,-1,-1,-2,-2,-2], | |
| "S":[-1,4,1,-1,1,0,1,0,0,0,-1,-1,0,-1,-2,-2,-2,-2,-2,-3], | |
| "T":[-1,1,4,1,-1,1,0,1,0,0,0,-1,0,-1,-2,-2,-2,-2,-2,-3], | |
| "P":[-3,-1,1,7,-1,-2,-1,-1,-1,-1,-2,-2,-1,-2,-3,-3,-2,-4,-3,-4], | |
| "A":[0,1,-1,-1,4,0,-1,-2,-1,-1,-2,-1,-1,-1,-1,-1,-2,-2,-2,-3], |