avrilcoghlan

package HelminthGenomeAnalysis::AvrilFastaUtils;

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

package HelminthGenomeAnalysis::AvrilFileUtils;

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

use base 'Exporter';
our @EXPORT_OK = qw( make_filename check_if_files_are_identical write_array_to_file );

avrilcoghlan

#!/usr/bin/env perl

=head1 NAME

    get_flanking_regions_of_genes.pl

=head1 SYNOPSIS
 
    get_flanking_regions_of_genes.pl input_gff input_fasta output_gff output_fasta outputdir flank_size
        where input_gff is the input gff file of gene predictions,

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

#!/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

#!/usr/local/bin/perl

=head1 NAME

    translate_spliced_dna.pl

=head1 SYNOPSIS
 
    translate_spliced_dna.pl spliced_dna translated_dna outputdir 
        where spliced_dna is the input fasta file of spliced DNA sequences for transcripts,

avrilcoghlan

YKL166C YIL033C
YCR002C	YHR107C
YCR002C	YJR076C
YCR002C	YLR314C
YJR076C	YHR107C

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_infer_ancestral_GOids3.pl
# Written by Avril Coghlan ([email protected])
# 3-May-07.  
#
# For the TreeFam project.
#
# This perl script infers the GO ids of ancestral nodes

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_infer_ancestral_GOids.pl
# Written by Avril Coghlan ([email protected])
# 2-Mar-07.  
#
# For the TreeFam project.
#
# This perl script infers the GO ids of ancestral nodes

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_infer_ancestral_features.pl
# Written by Avril Coghlan ([email protected])
# 30-May-07.  
#
# This perl script infers the features of ancestral nodes
# in a list of TreeFam trees, given the features in the
# leaves.