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@avrilcoghlan
avrilcoghlan / merge_optical_map_xml_files.py
Last active Aug 29, 2015
Python script for merging optical map xml files (for different scaffolds) into one large xml file
View merge_optical_map_xml_files.py
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
avrilcoghlan / find_bam_insertsize.pl
Last active Oct 12, 2015
Perl script to estimate the mean, median, standard deviation and IQR of insert sizes in a BAM file
View find_bam_insertsize.pl
#!/usr/bin/env perl
=head1 NAME
find_bam_insertsize.pl
=head1 SYNOPSIS
find_bam_insertsize.pl bam outputdir rpath
where bam is the input bam file,
@avrilcoghlan
avrilcoghlan / get_treefam_alns.pl
Last active Oct 12, 2015
Perl script to retrieve all multiple alignments for animal gene families from the TreeFam database
View get_treefam_alns.pl
#!/usr/local/bin/perl
=head1 NAME
get_treefam_alns.pl
=head1 SYNOPSIS
get_treefam_alns.pl treefam_version output outputdir
@avrilcoghlan
avrilcoghlan / translate_treefam_cigars_to_alns.pl
Last active Oct 12, 2015
Perl script to translate TreeFam cigar-format alignments to fasta-format alignments
View translate_treefam_cigars_to_alns.pl
#!/usr/local/bin/perl
=head1 NAME
translate_treefam_cigars_to_alns.pl
=head1 SYNOPSIS
translate_treefam_cigars_to_alns.pl treefam_version output outputdir cigars alntype start_with
@avrilcoghlan
avrilcoghlan / run_genewisedb_afterblast.pl
Last active Oct 12, 2015
Perl script to run GeneWise by comparing a file of multiple of HMMs to a fasta file of multiple sequences, by running GeneWise on the regions of the DNA sequences where the proteins used to make the HMM have tblastn matches
View run_genewisedb_afterblast.pl
This file has been truncated, but you can view the full file.
#!/usr/local/bin/perl
=head1 NAME
run_genewisedb_afterblast.pl
=head1 SYNOPSIS
run_genewisedb_afterblast.pl input_fasta input_hmms output outputdir spliceflat parameterfile treefam_seqs eval_cutoff flank_length blast_path
@avrilcoghlan
avrilcoghlan / get_treefam_family_seqs.pl
Last active Oct 12, 2015
Perl script to get all the protein sequences in a family in a particular version of the TreeFam database
View get_treefam_family_seqs.pl
#!/usr/local/bin/perl
=head1 NAME
get_treefam_family_seqs.pl
=head1 SYNOPSIS
get_treefam_family_seqs.pl treefam_version output outputdir core_only
where treefam_version is the version of TreeFam to use,
@avrilcoghlan
avrilcoghlan / overlap_alignment.pl
Created Nov 20, 2012
Perl script to get overlap alignment
View overlap_alignment.pl
#! /usr/bin/perl -w
# Avril Coghlan
# 20-Nov-2012
# Algorithm on page 204 of 'Computational Genome Analysis' by Deonier et al
# define the two sequences
$seqA = "AGGCTAAA";
$seqB = "CAAACGTCT";
print "Sequences:\n";
print "A: $seqA\n";
@avrilcoghlan
avrilcoghlan / embl_to_fasta.pl
Created Jan 7, 2013
Perl script to convert an embl format file to a fasta format file
View embl_to_fasta.pl
#!/usr/local/bin/perl
=head1 NAME
embl_to_fasta.pl
=head1 SYNOPSIS
embl_to_fasta.pl input_embl output_fasta outputdir
where input_embl is the input embl file,
@avrilcoghlan
avrilcoghlan / convert_chado_gff_to_gtf.pl
Last active Dec 10, 2015
Perl script to convert a gff file from the Chado database to a gtf format file for the RNA-SeqQC software
View convert_chado_gff_to_gtf.pl
#!/usr/local/bin/perl
=head1 NAME
convert_chado_gff_to_gtf.pl
=head1 SYNOPSIS
convert_chado_gff_to_gtf.pl input_gff output_gtf outputdir
where input_gff is the input embl file,
@avrilcoghlan
avrilcoghlan / find_best_genewise_genes.pl
Last active Dec 11, 2015
Perl script to take a gff file of gene predictions from GeneWise (or from some other program), and to make an output file with just the set of highest-scoring non-overlapping gene predictions.
View find_best_genewise_genes.pl
#!/usr/local/bin/perl
=head1 NAME
find_best_genewise_genes.pl
=head1 SYNOPSIS
find_best_genewise_genes.pl input_gff path_to_bedtools output_gff outputdir
where input_gff is the input GeneWise gff file,
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