avrilcoghlan

import os
import sys
from collections import defaultdict
import FiftyHG_Chembl

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

def main():

    # find the blast output files:  

avrilcoghlan

#!/usr/local/bin/perl

=head1 NAME

    calc_pc_id_between_seqs.pl

=head1 SYNOPSIS
 
    calc_pc_id_between_seqs.pl input_fasta output outputdir ggsearch
        where input_fasta is the input fasta file of sequences,

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

avrilcoghlan

#!/usr/local/bin/perl

=head1 NAME

    gff_to_genbank.pl

=head1 SYNOPSIS
 
    gff_to_genbank.pl input_gff assembly outputdir 
        where input_gff is the input gff file,

avrilcoghlan

import os
import sys
from Bio import Entrez
from Bio import SeqIO
import matplotlib.pyplot as plt

#====================================================================#
# Checked and seems to work fine.
# Takes the GenBank accession number (GI number) as input.
# First checks to see if the sequence has been stored locally as a file.

avrilcoghlan

#!/usr/bin/env perl

=head1 NAME

    convert_exonerate_gff_to_std_gff.pl

=head1 SYNOPSIS
 
    convert_exonerate_gff_to_std_gff.pl input_gff output_gff 
        where input_gff is the input exonerate gff file,

avrilcoghlan

#!/usr/bin/env perl

=head1 NAME

    run_exonerate_afterblast.pl

=head1 SYNOPSIS
 
    run_exonerate_afterblast.pl input_fasta input_pep output outputdir eval_cutoff flank_length blast_path type
        where input_fasta is the input fasta file of scaffolds in the assembly,

avrilcoghlan

#!/usr/bin/env perl

=head1 NAME

    make_exonerate_hints_for_augustus.pl

=head1 SYNOPSIS
 
    make_exonerate_hints_for_augustus.pl input_gff hints_file type
        where input_gff is the input exonerate gff file  

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):