avrilcoghlan

#!/usr/bin/perl
  
$file = $ARGV[0]; # input file of within-species paralogs from BioMart
open(FILE,"$file") || die "ERROR: cannot open $file\n";
while(<FILE>)
{
    $line = $_;
    chomp $line;
    @temp = split(/\t+/,$line);
    # Genome project  Gene stable ID  Paralogue gene stable ID

avrilcoghlan

import os
import sys
from collections import defaultdict
import FiftyHG_Chembl

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

def main():

    # find the blast output files:  

avrilcoghlan

import os
import sys
from collections import defaultdict
import FiftyHG_Chembl

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

def main():

    # find the blast output files:  

avrilcoghlan

import os
import sys
from collections import defaultdict
import FiftyHG_Chembl

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

def main():

    # find the blast output files:  

avrilcoghlan

import os
import sys
from collections import defaultdict
import FiftyHG_Chembl

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

def main():

    # find the blast output files:  

avrilcoghlan

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

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

# use the wormbase REST API to retrieve the phenotypes (from mutants, RNAi) for a particular gene:

def retrieve_phenotypes_from_wormbase(gene):

avrilcoghlan

# 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:

avrilcoghlan

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

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

# call the 'target prediction' API to find the predicted targets of our list of compounds:

def find_predicted_targets_of_compounds(cmpd_chembl_ids):

avrilcoghlan

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

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

avrilcoghlan

# 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" : ""})