Avril Coghlan avrilcoghlan

## retrieve_phenotypeinfo_from_wormbase.py
# script to retrieve the phenotype info for a particular gene from WormBase

import requests, sys

server = "http://rest.wormbase.org"
ext = "/rest/field/gene/WBGene00000079/phenotype"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})

if not r.ok:

## retrieve_genetrees_from_wormbase_parasite.py
import os
import sys
import requests # this is used to access json files
from ete3 import Phyloxml
import datetime

# Note: this script must be run in Python2 because ete3 uses Python2

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

## retrieve_smansoni_genelist_from_wormbase_parasite.py
# script to retrieve a list of all protein-coding Schistosoma mansoni genes from wormbase parasite
# example script taken from https://parasite.wormbase.org/rest-13/documentation/info/lookup_genome

import requests, sys

server = "https://parasite.wormbase.org"
ext = "/rest-13/lookup/genome/schistosoma_mansoni_prjea36577?biotypes=protein_coding"
# took the PRJEA from https://parasite.wormbase.org/Schistosoma_mansoni_prjea36577/Info/Index/

r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})

## pdb_rest_example_get_uniprot_for_pdbidlist.py
#!/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'

## "pdb_rest_example_get_pdbids_for_ligandidlist.py
#!/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'

## unichem_rest_example_get_pdbligandids_for_chemblidlist.py
#!/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:

## unichem_rest_example_get_pdbligandids_for_chemblid.py
#!/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:

## pdb_rest_example_get_pbids_with_ligand.py
#!/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'

## get_orths_from_newick_tree.pl
#!/usr/bin/perl

#---------------------------------------------------------------------------------------------#
#
# A Perl script to read a Newick tree file from Treefam, and
# print out the orthologues of a particular input gene.
#
# Avril Coghlan. 6-Dec-04.
# avril.coghlan@ucd.ie
#

## fix_embl_file_cds_error.py
import sys
import os
from collections import defaultdict

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

# read in the line numbers of dodgy CDS:

def read_error_file(error_file):
	# script to retrieve the phenotype info for a particular gene from WormBase

	import requests, sys

	server = "http://rest.wormbase.org"
	ext = "/rest/field/gene/WBGene00000079/phenotype"

	r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})

	if not r.ok:
	import os
	import sys
	import requests # this is used to access json files
	from ete3 import Phyloxml
	import datetime

	# Note: this script must be run in Python2 because ete3 uses Python2

	#====================================================================#
	# script to retrieve a list of all protein-coding Schistosoma mansoni genes from wormbase parasite
	# example script taken from https://parasite.wormbase.org/rest-13/documentation/info/lookup_genome

	import requests, sys

	server = "https://parasite.wormbase.org"
	ext = "/rest-13/lookup/genome/schistosoma_mansoni_prjea36577?biotypes=protein_coding"
	# took the PRJEA from https://parasite.wormbase.org/Schistosoma_mansoni_prjea36577/Info/Index/

	r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
	#!/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'
	#!/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:
	#!/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'
	#!/usr/bin/perl

	#---------------------------------------------------------------------------------------------#
	#
	# A Perl script to read a Newick tree file from Treefam, and
	# print out the orthologues of a particular input gene.
	#
	# Avril Coghlan. 6-Dec-04.
	# avril.coghlan@ucd.ie
	#
	import sys
	import os
	from collections import defaultdict

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

	# read in the line numbers of dodgy CDS:

	def read_error_file(error_file):