Avril Coghlan avrilcoghlan

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Wellcome Trust Sanger Institute
Cambridge, U.K.
http://www.sanger.ac.uk/research/projects/parasitegenomics/

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avrilcoghlan / pdb_rest_example_get_uniprot_for_pdbidlist.py

Created June 18, 2019 11:18

script to retrieve UniProt ids for an input list of PDB ids.

	#!/usr/bin/env python
	# example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
	# edited to use the python 'requests' module, and to get the UniProt id. for particular PDBe entry ids

	import argparse
	import sys
	import requests # this is used to access json files

	PY3 = sys.version > '3'

avrilcoghlan / pdb_rest_example_get_uniprot_for_pdbid.py

Created June 18, 2019 10:37

script to retrieve the UniProt id for a particular PDB id

	#!/usr/bin/env python
	# example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
	# edited to use the python 'requests' module, and to get the UniProt id. for a particular PDBe entry id.

	import argparse
	import sys
	import requests # this is used to access json files

	PY3 = sys.version > '3'

avrilcoghlan / "pdb_rest_example_get_pdbids_for_ligandidlist.py

Created June 18, 2019 10:15

Script to retrieve PDB entry ids for PDB entries that contain PDB ligand ids in an input list of PDB ligand ids.

	#!/usr/bin/env python
	# example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
	# edited to use the python 'requests' module, and to get the PDB ids. for an input list of PDB ligand ids.

	import argparse
	import sys
	import requests # this is used to access json files

	PY3 = sys.version > '3'

avrilcoghlan / unichem_rest_example_get_pdbligandids_for_chemblidlist.py

Created June 18, 2019 09:21

Script to retrieve the PDB ligand ids. for a list of input ChEMBL compounds

	#!/usr/bin/env python
	# script to find out the PDB three-letter ligand id. for a ChEMBL id., using UniChem

	import argparse
	import sys
	import requests # this is used to access json files

	PY3 = sys.version > '3'

	if PY3:

avrilcoghlan / unichem_rest_example_get_pdbligandids_for_chemblid.py

Created June 17, 2019 11:39

Script to use the UniChem REST API to get the PDB ligand identifier for a particular ChEMBL identifier

	#!/usr/bin/env python
	# script to find out the PDB three-letter ligand id. for a ChEMBL id., using UniChem

	import argparse
	import sys
	import requests # this is used to access json files

	PY3 = sys.version > '3'

	if PY3:

avrilcoghlan / pdb_rest_example_get_pbids_with_ligand.py

Created June 17, 2019 10:58

Use the PDB REST API to get a list of PDB entries that contain a particular ligand

	#!/usr/bin/env python
	# adapted example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
	# edited to use the python 'requests' module

	import argparse
	import sys
	import requests # this is used to access json files

	PY3 = sys.version > '3'

avrilcoghlan / retrieve_bioactivity_info_from_chembl.py

Created May 30, 2019 10:11

Python script to query the ChEMBL database to retrieve a list of compounds with bioactivities for certain target proteins, and then retrieve information on the molecular properties of those compounds

	import pandas as pd # uses pandas python module to view and analyse data
	import requests # this is used to access json files

	#====================================================================#

	# using a list of known targets, find compounds that are active on these targets:

	def find_bioactivities_for_targets(targets):

	targets = ",".join(targets) # join the targets into a suitable string to fulfil the search conditions of the ChEMBL api

avrilcoghlan / Find_compounds_for_NTD_targets_and_filter_those_compounds.ipynb

Created May 29, 2019 09:56

Python notebook to query ChEMBL, to retrieve compounds with bioactivities for certain targets, and obtain properties of those compounds

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avrilcoghlan / fix_embl_file_cds_error.py

Created November 28, 2018 10:04

Script to correct EMBL files so that CDSs with >50% internal Ns are marked as /pseudo

	import sys
	import os
	from collections import defaultdict

	#====================================================================#

	# read in the line numbers of dodgy CDS:

	def read_error_file(error_file):

avrilcoghlan / list_dogdy_genes_in_embl_file.py

Created November 28, 2018 09:44

Script to make a list of dodgy genes in an EMBL file, based on the VAL_ERROR.txt file produced by the ENA's file validator

	import sys
	import os
	from collections import defaultdict

	#====================================================================#

	# read in the set of lines with dodgy genes on them in the embl file:

	def read_lines_with_dodgy_genes(input_error_file):

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