avrilcoghlan

#!/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

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

#!/usr/bin/env perl

=head1 NAME

    rename_genes_in_maker_gff.pl       

=head1 SYNOPSIS
 
    rename_genes_in_maker_gff.pl input_gff output_gff outputdir species  
        where input_gff is the input gff file,

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_genelosses.pl
# Written by Avril Coghlan (alc@sanger.ac.uk).
# 28-Aug-06.  
#
# For the TreeFam project.
#
# This perl script connects to the MYSQL database of

avrilcoghlan

import sys
import os
from xml.etree import ElementTree as ET
import AvrilFileUtils

class Error (Exception): pass

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

# define a function to merge optical map xml files for different scaffolds.

avrilcoghlan

#!/usr/local/bin/perl

=head1 NAME

    run_genewisedb_afterblast.pl

=head1 SYNOPSIS
 
    run_genewisedb_afterblast.pl input_fasta input_hmms output outputdir spliceflat parameterfile treefam_seqs eval_cutoff flank_length blast_path
        where input_fasta is the input fasta file of scaffolds,

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: