epaule

#!/usr/bin/env python3
# usage: python3 hap_bedgraph.py FASTA > BEDGRAPH

import sys
import re
from Bio import SeqIO
ns=re.compile("[Nn]+")
for seq_record in SeqIO.parse(sys.argv[1], "fasta"):
    for m in ns.finditer(str(seq_record.seq)):
        print(f'{seq_record.id}\t{m.start()}\t{m.end()+1}\t200')

epaule

#!/bin/bash

# Tom Mathers.

# Script to map hap2 chromosome (SUPER) IDs to hap1 IDs for genomeark assemblies.

# Script aligns hap2 to hap1 with mashmap and selects the longest alignment per chrom. Only scaffolds with SUPER IDs are included in the output mapping.

## NOTE - the script filters out sex known sex chromsomes (X, Y, Z and W). These are not reported in the final mapping file.

epaule

#!/usr/bin/env ruby
# usage: ruby remove_id_from_fasta.rb FILE_WITH_IDS FASTA_FILE

require 'bio'

ids = []
File.foreach(ARGV.shift, chomp: true) do |line|
 ids << line
end

epaule

#!/nfs/users/nfs_m/mh6/.linuxbrew/homebrew/bin/ruby
# usage:  ruby get_rnaseq_number_for_species.rb "Xestospongia muta"

require "net/http"
require "uri"
require "cgi"

species = ARGV[0]

species = CGI.escapeURIComponent(species)

epaule

#!/bin/env perl
open IN,shift;
while(<IN>){
	push @h,"$1" if />(\S+)/
}
close IN;
open IN,shift;
while(<IN>){
	@F=split;
	next unless $F[2] eq 'CDS';

epaule

#!/usr/bin/env crystal
require "http/client"
require "json"

species = ARGV[0]

species = species.gsub(/\s/, "%20")

r = HTTP::Client.get("https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/#{species}", headers: HTTP::Headers{"Accept" => "application/json"})
raise "cannot get the taxonomy" unless r.success?

epaule

#!/usr/bin/env ruby
# frozen_string_literal: true

# add > signs to the nearest gaps in a TPF based on AGP breaks
# usage: ./mark_scaffolds.rb -a AGP -t TPF -o TPF2

require 'optparse'

# get the gaps from the AGP as Hash of Arrays [seq_id] => [1,2,3]
def parse_agp(file)

epaule

Step 9 - Rename and re-run maps
It is likely that between the pairs of chromosomes there will be discrepancies in size. This will result in the files being in different orders when they get size sorted. This needs to be corrected before submission. The can be done manually or using the following method:  

Run: 
bsub -G grit-grp -n 16 -e e_hap2hap_mapping -o o_hap2hap_mapping -M 16000 -R 'select[mem>16000] rusage[mem=16000] span[hosts=1]' sh /software/grit/projects/vgp_curation_scripts/hap2_hap1_ID_mapping.sh <h1_fasta> <h2_fasta>


Then:
/software/grit/projects/vgp_curation_scripts/update_mapping.rb -c <renamed_hap2_chroms.csv> -f <hap2.fa> -t <hap2_hap1.tsv> > hap2.renamed.fa

epaule

#!/bin/bash

# simple files
for f in *.bed *.contamination *recommendation *report.txt *taxonomy.rpt */*/*combined_summary.csv *.fa *.gb
do
    perl -i_original -pne 's/scaffold_/SCAFFOLD_/' $f
done

# compressed fastas
for f in *.gz

epaule

#!/bin/bash

# Script by Tom Mathers. 

# Script requires 32 cores and ~50Gb ram (depending on genome size).
# Seqkit and BUSCO need to be in path.
# Scaffold IDs need to be in final tol format. 
# Query and ref short IDs need to be two letter codes eg. "Ac". 
# Query and ref fasta files need to be in working dir.