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@RasmusFonseca
RasmusFonseca / flareplot-main.js
Created May 9, 2019
Flareplot main script with tracks moved toward center
View flareplot-main.js
/**
* 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
RasmusFonseca / sysusg.py
Last active Jul 2, 2018
Monitor CPU-time and max memory usage using ps
View sysusg.py
"""
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
RasmusFonseca / multiproducer-consumer.py
Last active May 7, 2018
Python multiple producer / single consumer example
View multiproducer-consumer.py
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:
View scrollable-table.html
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<title>Document</title>
<style>
* {
box-sizing: border-box;
}
td, th{
View flareplot-selectors1.js
/**
* 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">
View momentconfig.json
{
"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"
View momentmetadata.tsv
We can make this file beautiful and searchable if this error is corrected: No tabs found in this TSV file in line 0.
100D
101D
102D
103D
104D
109D
10MH
111D
112D
113D
View allmoments.tsv
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.
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
RasmusFonseca / extractFeatures.py
Created Jan 2, 2017
Extracting protein features as .tsv using blosum62 from a fasta file
View extractFeatures.py
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],
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