avrilcoghlan

#!/usr/bin/env perl

# Get the families predicted for the human gene ENSG00000139618. What do you notice ?
# Note: Families include UniProt proteins and Ensembl genes/proteins.

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

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

avrilcoghlan

#!/usr/bin/env perl

# Get the multiple alignment corresponding to the family with the stable id ENSFM00250000006121
# Note: this prints some warnings about uninitialised values in the Compara api

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

avrilcoghlan

#!/usr/bin/env perl

# Find and print the sequence of all the peptide Members corresponding to the human protein-coding gene(s) FRAS1.
# Print its attributes using the print_member() method. 
# Get all the peptide members and print them as well. 
# Print the sequence of these members.

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

avrilcoghlan

#!/usr/bin/env perl

# Print the sequence of the Member corresponding to SwissProt protein O93279

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

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

avrilcoghlan

# define function 'xrange'

def xrange(x):
   
    return iter(range(x))

genes = ['g0', 'g1', 'g2', 'g3', 'g4', 'g5', 'g6', 'g7', 'g8', 'g9', 'g10', 'g11']

# create a list containing 12 lists initialised to 0
Matrix = [[0 for x in xrange(12)] for x in xrange(12)]

avrilcoghlan

# define function 'xrange'

def xrange(x):

    return iter(range(x))

genes = ['g1', 'g2', 'g3', 'g4', 'g5', 'g6', 'g7']
Matrix = [[0 for x in xrange(7)] for x in xrange(7)]
Matrix[1-1][4-1] = 12
Matrix[4-1][1-1] = 12

avrilcoghlan

package HelminthGenomeAnalysis::AvrilGenefindingUtils;

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

import sys
from Bio import SeqIO

#====================================================================#
# check the command-line arguments:
if len(sys.argv) != 2:
    print("Usage: %s sff_file") % sys.argv[0]
    sys.exit(1)

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

avrilcoghlan

#!/usr/bin/env perl

=head1 NAME

    split_up_fasta.pl

=head1 SYNOPSIS
 
    split_up_fasta.pl input_fasta num_seqs_per_file prefix outputdir
        where input_fasta is the input fasta file,

avrilcoghlan

#!/usr/bin/env perl

=head1 NAME

    merge_overlapping_exons.pl

=head1 SYNOPSIS
 
    merge_overlapping_exons.pl input_gff output_gff outputdir input_fasta
        where input_gff is the input gff file,