Eric Weitz eweitz

Genomes, JavaScript, Python

eweitz / http_debugging.py

Last active November 12, 2022 20:32 — forked from tonetheman/http_debugging.py

Debug requests for urllib in Python 3

	"""" Tested in Python 3.4 """

	import urllib.request
	import http.client

	http.client.HTTPConnection.debuglevel = 1

	response = urllib.request.urlopen('https://github.com/eweitz')

eweitz / ncbi_sequence_viewer_plasmodium.html

Last active June 16, 2016 04:04

Plasmodium falciparum chromosome 1 in NCBI Sequence Viewer

	<!DOCTYPE html>
	<html>
	<head>
	<!-- Include sviewer.js. Don't forget id="autoload"! -->
	<script type="text/javascript" src="https://www.ncbi.nlm.nih.gov/projects/sviewer/js/sviewer.js" id="autoload"></script>
	</head>
	<body>
	<h1>NCBI Sequence Viewer: Plasmodium falciparum strain 3D7, chromosome 1</h1>
	<!--
	Sequence Viewer Embedding API: https://www.ncbi.nlm.nih.gov/tools/sviewer/embedding-api/

eweitz / protein_hgvs_for_snp_id.py

Last active January 28, 2019 03:14

How to get protein change HGVS data for a given dbSNP RS ID, using NCBI EUtils

	"""Python 3 script to get partial protein HGVS given NCBI dbSNP ID

	Example:

	$ python3 protein_hgvs_for_snp_id.py 334
	snp_id:
	334
	gene:
	{'name': 'HBB', 'gene_id': '3043'}
	protein_change_hgvs:

eweitz / chr_rs_acc_via_eutils.py

Created April 25, 2017 15:33

NCBI EUtils demo: get a chromosome's RefSeq accession given its name and assembly

	'''
	This simple script shows how to use NCBI E-Utilies to get a chromosome's
	RefSeq accession given the chromosome's name and its genome assembly.

	Example:
	$ python3 chr_rs_acc_via_eutils.py
	RefSeq accession for chromosome 6 on genome assembly GRCh38 (GCF_000001405.26):
	NC_000006.12
	'''

eweitz / extract_scp_study_metadata.py

Last active February 1, 2019 15:03

Extract study metadata using Python bindings for Single Cell Portal REST API

	"""Extract public study metadata using Python bindings for SCP REST API

	See https://github.com/broadinstitute/single_cell_portal/issues/52 for context and usage notes.
	"""

	import argparse
	import json
	import pprint

	import scp_api

eweitz / wikipathways-by-organism.sh

Last active June 9, 2021 12:44

Pathway count by organism in WikiPathways

	# Get number of pathways by organism in WikiPathways
	# Graph of output:
	# https://docs.google.com/spreadsheets/d/1zZSqeKufuYxfFd3pFeMAUOjCm1sLRAw5SgJ4OJel9M8/edit?usp=sharing

	# Fetch all organisms in WikiPathways
	curl -s https://webservice.wikipathways.org/listOrganisms?format=json \| jq .organisms[] > organisms-wikipathways.json

	# Fetch all pathways in WikiPathways
	curl -s https://webservice.wikipathways.org/listPathways?format=json \| jq . > all-wikipathways.json

eweitz / wikipathways-review.js

Last active July 22, 2024 12:10

Summarize recent changes in WikiPathways

	// This JavaScript code helps summarize recent changes for WikiPathways
	// See output at e.g. https://github.com/wikipathways/wikipathways-help/discussions/124
	//
	// To run:
	// - Go to https://classic.wikipathways.org/index.php?title=Special:RecentPathwayChanges&limit=500&offset=0
	// - Open Developer Tools in your web browser
	// - Update the `dates` array below
	// - Execute code, e.g. by putting cursor at end of last line and pressing Return / Enter
	//
	// The output can be pasted into the "Recent changes" section for new Weekly Review Report entries

eweitz / uncommon_ontology_chars.py

Created August 2, 2024 17:49

Find less common string characters in Cell Ontology

	"""Find less common string characters in Cell Ontology

	Prints characters that aren't an ASCII letter, number, hyphen, space, or
	underscore that appear among standard labels in Cell Ontology (CL).
	This snippet helps get testing input for more robust ontology handling.

	Tested on Python 3.10.9, without dependencies. Output as of 2024-08-02:
	.=/[:]–><';,()+
	"""