antonkratz

# author:   Anton Kratz
# created:  Mon Dec 17 19:08:48 PST 2018

# Based on original code by Mike Yu which is at [1]. However [1] has various NDEX and other
# code intermingled which is not necessary in this context. Also, I am building a similarity
# table for DNA repair on the fly.

# [1] https://github.com/michaelkyu/ddot/blob/master/examples/Process_the_Gene_Ontology.ipynb

import requests

antonkratz

Cytoscape 3.7.1

the layout is too dense and I want to expand the layout

Layout --> Node layout Tools --> Scale:

when I zoom out, the text on the label dissappears

antonkratz

Delete all lines in the file myfile that contain the string foobar:

sed -i '/foobar/d' myfile

antonkratz

file1: A list of keys, one key one line

file2: A table, the keys are in column 1

what this does: pull out the lines from the table which match a key from a list

time awk -F'      ' 'NR==FNR{c[$1]++;next};c[$1] > 0' file1 file2 > output.txt

antonkratz

conda adds an uncalled for (base) before my PS1 prompt. Most solutions suggest to edit the .condarc file. This did not work for me. Instead:

conda config --set auto_activate_base False

https://askubuntu.com/questions/1026383/why-does-base-appear-in-front-of-my-terminal-prompt

antonkratz

Select All
`Object > Clipping mask > Release`
`Object > Path > Clean up`

Clipping masks. Deleting an object deletes random objects scattered throughout b.c they are connected thru the clipping mask. I do not want this.

antonkratz

import pubchempy as pcp
import pandas as pd
import numpy as np
from collections import OrderedDict

drugs_df = pd.read_csv('oli_drugs.csv')

def queryPubChem(compounds,batchlist = None,match='name'):
    """
    This function queries the PubChem database to retrieve both the isomeric smile and CID of a compound.

antonkratz

x = c(0.8846, 1.1554, 0.9317, 0.9703, 0.9053, 0.9454, 1.0146, 0.9012, 0.9055, 1.3307)
y = c(0.9828, 1.0329, 0.931, 1.3794, 0.9273, 0.9605, 1.0259, 0.9542, 0.9717, 0.9357)
ShortSci = c("MotAlb", "PruMod", "EriRub", "LusMeg", "PhoOch", "PhoPho", 
         "SaxRub", "TurMer", "TurPil", "TurPhi")
df <- data.frame(x = x, y = y, z = ShortSci)
 
library(ggplot2)
library(ggrepel)
p1 <- ggplot(data = df, aes(x = x, y = y)) + theme_bw() + 
  geom_text_repel(aes(label = z), 

antonkratz

#' symlog transformation
#'
#' `symlog_trans()` transforms data using `log(x)` for `abs(x) > thr`, where
#' `thr` is a tuneable threshold, but leaves the data linear for `abs(x) < thr`.
#' (credit for base code to https://stackoverflow.com/users/1320535/julius-vainora)
#'
#'
#' @param base base of logarithm
#' @param thr numeric threshold for transitioning from log to linear
#' @param scale numeric scaling factor for data

antonkratz

Google Hacks: Gmail, Docs

Gmail

Bookmarks to emails are persistent

You can bookmark individual emails. The bookmarks are persistent, apparently indefinitely (works for me with bookmarks made several years ago).

Add a 30 second delay before the email is actually sent