avrilcoghlan

#!/usr/bin/env perl

=head1 NAME

    find_best_nonoverlapping_genes.pl

=head1 SYNOPSIS
 
    find_best_nonoverlapping_genes.pl input_gff path_to_bedtools output_gff outputdir min_gene_score from_maker subtract_from
        where input_gff is the input GeneWise gff file,

avrilcoghlan

#!/usr/bin/env perl

=head1 NAME

    remove_tiny_genes_from_gff.pl      

=head1 SYNOPSIS
 
    remove_tiny_genes_from_gff.pl input_gff output_gff min_length outputdir assembly
        where input_gff is the input gff file,

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/bin/env perl

=head1 NAME

    remove_modelgff_genes_from_gff.pl      

=head1 SYNOPSIS
 
    remove_modelgff_genes_from_gff.pl input_gff output_gff 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

    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

#!/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

package HelminthGenomeAnalysis::AvrilGffUtils;

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( read_gene_ids replace_gene_ids_in_gff get_gff_lines_for_feature_types add_flanking_region_to_gff_features make_fasta_for_gff make_gff_for_features_in_subsequences read_genenames_for_transcripts get_gene_name add_gene_features_to_gff_for_subsequences make_gff_for_features_in_sequences sort_gff merge_overlapping_cds sort_gff_lines_for_genes count_features_in_region convert_exonerate_gff_to_standard_gff );

avrilcoghlan

package HelminthGenomeAnalysis::AvrilAlignUtils;

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);