ar0ch

"""Quick and dirty transform of the Zola guest list CSV export to formatted addresses"""

import csv
from dataclasses import dataclass
from pathlib import Path
from typing import Optional, Union


@dataclass
class Address:

ar0ch

#!/bin/bash
year=2020
for i in {1..3}; do
	for j in {WebServer,ComparativeGenomics,FunctionalAnnotation,GenePrediction,GenomeAssembly};do 
		gh repo create -t compgenomics${year} Team${i}-${j}
		git clone  git@github.gatech.edu:compgenomics${year}/Team${i}-${j}.git
		cd Team${i}-$j; 
		git remote add github git@github.com:compgenomics${year}/Team${i}-$j;
		git push -u github master;
		cd ../

ar0ch

#!/bin/bash
mkdir lgen plnk vcf
for i in folder_of_CELs/*;do 
	j=`basename $i`
	cat $i |tail -n +14 | pee "awk -F '\t' '{print \"FAMID\",\$1,\$2,\$5,\$6}' > lgen/$j.lgen" \
							  "awk -F '\t' '{print \$3,\$2,'0',\$4}' > lgen/$j.map" \
							  "awk -F'\t' '{print "FAMID",$1,'0','0','0','0'}' > lgen/$j.fam"
	plink --lgen lgen/$j.lgen --fam lgen/$j.fam --map lgen/$j.map --make-bed --out plink/$j
	plink --lgen lgen/$j.lgen --fam lgen/$j.fam --map lgen/$j.map --recode vcf --out vcf/$j
done

ar0ch

#!/usr/bin/env python
import sys
import os
import re
import shutil
import xml.etree.ElementTree as ET
try:
    from urllib.request import urlopen, urlretrieve
except ImportError:
    from urllib import urlopen, urlretrieve

ar0ch

library(shiny)
# Also uses parallel, shinyjs, tools

# Create a long-running task, executed in a forked process. (Doesn't work on Windows)
# 
# The return value is a promise-like object with three
# methods:
# - completed(): FALSE initially, then TRUE if the task succeeds,
#   fails, or is cancelled. Reactive, so when the state changes
#   any reactive readers will invalidate.

ar0ch

>NC_011283.1
gttcgagtggagtccgccgtgtcactttcgctttggcagcagtgtcttgc
ccgattgcaggatgagttaccagccacagaattcagcatgtggatccgcc
cattgcaggcggaactgagcgataacacgctggcactgtatgcgccaaac
cgttttgtgctcgactgggtaagggacaaatacctcaataatatcaatgg
actcctcaatgacttttgcggtgctgatgccccgcagctgcgttttgagg
tgggtgctaagccagccagctcgctgcagaaaggagcggtaagcccggct
gcggcggccattccggcggcgcaggtgcagaccgcgcgcgtggcgccgac
gatcgtgcgcccaggctgggataatgtcccggcgccagcggagccgacct
accgctctaacgttaacgtgaaacacacgtttgataacttcgtcgaaggt

ar0ch

>NC_011283.1:1770808-1774323
atgtccggaaacatgaaaacaatggatggcaacacggcggcggcctggatctcctacgcc
tttaccgacgtggcggccatctaccccatcaccccctccacgccgatggcggaaaatgtc
gatgaatgggccgctaaggggaaaaagaatctgtttggccagccggtgcgcctgatggag
atgcaatccgaagccggtgccgccggggcggtgcacggcgcgctgcaggcgggagcgctc
accaccacctacaccgcgtcgcaggggctgctgctgatgatccccaatttgtacaaaatt
gccggtgaactgctgccgggtgtttttcacgtcagcgcgcgggcgctggcgaccaattcg
ctgaatatttttggcgaccaccaggacgtgatggcggtacggcagaccggctgcgccatg
ctggtggagaataacgttcagcaggtgatggacctgtcggcggtggcgcacctggcggcg
atcgccgggcggatcccgtttatcaactttttcgacggctttcgcacctcgcacgaaata

ar0ch

>Illumina_DpnII_expression_PCR_Primer_2
AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
>Illumina_Single_End_Sequencing_Primer
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>custom3
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Illumina_DpnII_expression_Sequencing_Primer
CGACAGGTTCAGAGTTCTACAGTCCGACGATC
>Illumina_Multiplexing_PCR_Primer_2.01
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT

ar0ch

From 96c2f53e77c6898132fb0e6c89ce4433a35c31bc Mon Sep 17 00:00:00 2001
From: Aroon Chande <git@atc.io>
Date: Tue, 24 Oct 2017 09:52:30 -0400
Subject: [PATCH] Update Unicycler
 - Add racon and miniasm run dependencies
 - Set py27 incompatible

---
 recipes/unicycler/meta.yaml |    8 +++++---
 1 files changed, 5 insertions(+), 3 deletions(-)

ar0ch

staticperl mkperl -MConfig::Simple -MPod::Usage -MGetopt::Long -MFile::Path -Mwarnings --use Config_heavy.pl -v --add "abil/nasp.pm" -v