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

import sys
import os
from collections import defaultdict

class Error (Exception): pass

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

# define a function to read in the ancestors of each GO term in the GO hierarchy:

avrilcoghlan

import sys
import os
from collections import defaultdict
from scipy.sparse import lil_matrix # needed for Dijkstra's algorithm
from scipy.sparse.csgraph import dijkstra # needed for Dijkstra's algorithm

class Error (Exception): pass

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

avrilcoghlan

def DFS_dist_from_node(query_node, parents):
    """Return dictionary containing distances of parent GO nodes from the query"""
    result = {}
    stack = []
    stack.append( (query_node, 0) )
    while len(stack) > 0:
        print("stack=", stack)
        node, dist = stack.pop()
        result[node] = dist

avrilcoghlan

package HelminthGenomeAnalysis::AvrilHMMUtils;

use strict;
use warnings;
use Bio::Seq;
use Bio::SeqIO;
use Moose;
use Math::Round; # HAS THE nearest() FUNCTION
use Carp::Assert; # HAS THE assert() FUNCTION 
use Scalar::Util qw(looks_like_number);

avrilcoghlan

#!/usr/bin/env perl

=head1 NAME

    parse_hmmpfam_output.pl

=head1 SYNOPSIS
 
    parse_hmmpfam_output.pl hmmpfam protein_fasta evalue_cutoff total_num_hmms cegma_dir
        where hmmpfam is the hmmpfam output file,

avrilcoghlan

#!/usr/bin/env perl

# Count the number of “one2one” orthologues between human and mouse
# Note: this script gives a warning about some variable declaration within the Compara API.

use strict;
use warnings;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

avrilcoghlan

#!/usr/bin/env perl

# Get all the homologues for the human gene ENSG00000229314
# Note: get a warning about a variable declaration in the Compara API when this script is run.

use strict;
use warnings;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

avrilcoghlan

#!/usr/bin/env perl

# Print all the members of the tree containing the human ncRNA gene ENSG00000238344

use strict;
use warnings;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

avrilcoghlan

#!/usr/bin/env perl

# Print the protein tree with the stable id ENSGT00390000003602

use strict;
use warnings;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';