rhngla’s gists

rhngla / 00-gene-ensembl.py

Last active January 22, 2024 22:40

gget to search for Ensembl ids of gene names

	# Some gene names have aliases; those can be found using gget.

	import gget
	import pandas as pd

	gene_list = ['1190002N15Rik', '1700019L22Rik', '1700086L19Rik', '2610100L16Rik', '2900055J20Rik', '2900092D14Rik', '3110035E14Rik', '5031426D15Rik', '5930412G12Rik', '6330403A02Rik', '6430573F11Rik', 'A230070E04Rik', 'A330050F15Rik', 'AF529169', 'Ak3l2-ps', 'Apitd1', 'BC030499', 'BC048546', 'Bai2', 'Cecr6', 'Ctgf', 'Cxx1a', 'E130012A19Rik', 'E530001K10Rik', 'Epb4.1', 'Epb4.1l4a', 'Fam150b', 'Fam196a', 'Fam19a1', 'Fam19a2', 'Fam19a5', 'Fam212b', 'Fam46a', 'Fam84a', 'Fam84b', 'Gad1-ps', 'Gpr123', 'Gpr125', 'Gpr126', 'Gpr133', 'Gucy1a3', 'Hrasls', 'Hyi', 'I830012O16Rik', 'LOC100503338', 'LOC101056001', 'LOC102632463', 'LOC102633357', 'LOC102633724', 'LOC102634132', 'LOC102634502', 'LOC102635502', 'LOC102636041', 'LOC102636700', 'LOC102638670', 'LOC102638890', 'LOC102640573', 'LOC102643175', 'LOC105242578', 'LOC105242710', 'LOC105242740', 'LOC105243130', 'LOC105243282', 'LOC105243425', 'LOC105243542', 'LOC105244000',

rhngla / GO_terms.csv

Last active August 8, 2023 17:50

Pathways and Genes

	GO_id	description
	GO:0006623	protein targeting to vacuole
	GO:0006626	protein targeting to mitochondrion
	GO:0006627	protein processing involved in protein targeting to mitochondrion
	GO:0006672	ceramide metabolic process
	GO:0031647	regulation of protein stability
	GO:0006744	ubiquinone biosynthetic process
	GO:0006734	NADH metabolic process
	GO:0006783	heme biosynthetic process
	GO:0006506	GPI anchor biosynthetic process

rhngla / TreeLengths.m

Created July 8, 2020 19:31

Calculate tree lengths for trees in the graph specified by (AM,r)

	function tree_lengths=TreeLengths(AM,r)
	%Returns total length measured for each of the L trees defined by the labeled adjacency matrix.
	%Inputs:
	% AM : (NxN) matrix labeled adjacency matrix (assumed symmetric)
	% r : (Nx3) position vector for the N nodes
	%Outputs:
	% tree_lengths : (1xL)

	AMlbl_direct=triu(AM,1);
	tree_labels=unique(AMlbl_direct(AMlbl_direct>0));

rhngla / pathlib_examples.py

Created July 3, 2020 19:49

pathlib examples

	#Some simple file IO related operations

	from pathlib import Path

	#Below takes care of os based differences
	dir_name = '/Users/Fruity/Local/datasets'
	file_name = 'CTX_Hip_10x_counts.h5'

	dir_path = Path(dir_name)
	#Use forward slashes to combine path

rhngla / gist:1fa633a3df46e07b26c6db24d9c0a7a6

Created May 13, 2020 15:23

gif from png stack

	sudo apt-get install imagemagick
	convert -delay 200 -loop 0 *.png output.gif

	#Order of files as specified in file_list.txt
	convert -delay 20 @file_list.txt -loop 0 animation.gif

rhngla / CCA_extended.py

Last active March 25, 2020 07:06

Extend the CCA class of scikit-learn to return reconstructions of the Y as well.

	from sklearn.cross_decomposition import CCA
	from sklearn.utils import check_array
	from sklearn.utils.validation import check_is_fitted, FLOAT_DTYPES

	class CCA_extended(CCA):

	def __init__(self,args,*kwargs):
	super().__init__(args,*kwargs)
	return

rhngla / tricks.py

Last active June 27, 2019 23:42

Python tricks

	#Ref: http://akuederle.com/create-numpy-array-with-for-loop
	import numpy as np
	n_results_per_iter = 4
	result_array = np.empty((0, n_results_per_iter))
	for iter in [1,2,3]:
	result_this_iter = np.array([0,1,2,3])
	result_array = np.append(result_array, [result_this_iter], axis=0)


	#Slicing rows and columns from a matrix simultaneously. The key is to use broadcasting.

rhngla / startupscript.py

Last active July 27, 2022 23:04

IPython startup script

	#File will be executed for every new instance of ipython
	#Place file in: ~/.ipython/profile_default/startup/startupscript.py
	print('loading packages and magics from ~/.ipython/profile_default/startup/startupscript.py')
	from IPython import get_ipython

	get_ipython().run_line_magic("load_ext","autoreload")
	print('%load_ext autoreload')
	get_ipython().run_line_magic("autoreload", "2")
	print('%autoreload 2')

Rohan rhngla