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import sys | |
THRESHOLD = 0.25 # reads must have 25% of their k-mers assigned | |
for line in sys.stdin: | |
fields = line.strip().split() | |
kmers_fields = fields[4:] | |
total_kmers = sum([int(x.split(":")[1]) for x in kmers_fields]) | |
unassigned_kmers = sum([int(x.split(":")[1]) for x in kmers_fields if x[0] == "0"]) |
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# A little bash script to download our juicy ONT PION data | |
# If this doesn't work for you, express your disappointment to @samstudio8. | |
# Use "EVEN" or "LOG" for $1, eg: `bash get_pion_signal.sh EVEN` | |
MODE=$1 | |
echo "Fetching signal blocks. Don't be afraid to CRTL+C and resume if needed..." | |
for i in {00..25} | |
do | |
echo $i; | |
wget -c https://nanopore.s3.climb.ac.uk/Zymo-PromethION-$MODE-BB-SN_signal.tar.$i; |
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# grab an off the shelf container with cuda9 | |
FROM nvidia/cuda:9.0-devel-ubuntu16.04 | |
# update gcc to gcc-6 as the default gcc-5 is too old | |
RUN apt-get update && apt-get install -y software-properties-common wget git | |
RUN add-apt-repository ppa:ubuntu-toolchain-r/test | |
RUN apt-get update && apt-get install -y gcc-6 g++-6 | |
# update cmake as the default is too old | |
RUN wget -qO- "https://cmake.org/files/v3.15/cmake-3.15.1-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C /usr/ |
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library(tidyverse) | |
assemblies=read_tsv('kraken_summary.bond.tsv') | |
short_name <- c( | |
"Bacillus subtilis" = "bs", | |
"Cryptococcus neoformans" = "cn", | |
"Enterococcus faecalis" = "ef", | |
"Escherichia coli" = "ec", | |
"Lactobacillus fermentum" = "lf", |
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import argparse | |
import sys | |
import random | |
import numpy as np | |
import pysam | |
parser = argparse.ArgumentParser(description="A very very very bad read generator.") | |
parser.add_argument("shred", type=int) | |
parser.add_argument("fasta") |
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rm counties.* | |
rm *csv | |
# England ###################################################################### | |
curl -O -J -L https://www.registers.service.gov.uk/registers/local-authority-eng/download-csv | |
# https://www.datadictionary.nhs.uk/data_dictionary/nhs_business_definitions/l/local_authority_de.asp? | |
# A Local Authority, in relation to England is: | |
## a County Council | |
awk -F',' '$6=="CTY" {print $7}' local-authority-eng.csv >> counties.eng.ls |
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#!/bin/bash | |
USER_ID=${LOCAL_USER_ID:-9001} | |
echo "starting with UID : $USER_ID" | |
echo "creating RAMPART user" | |
useradd --shell /bin/bash -u $USER_ID -o -c "" -m rampart | |
echo "raising RAMPART on $CLIENT $SERVER" |
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# kraken2-microbial database | |
## Monday 3rd September 2018 | |
## s.nicholls.1 | |
KDB=$1 | |
kraken2-build --download-taxonomy --threads 24 --db $KDB | |
kraken2-build --download-library archaea --db $KDB | |
kraken2-build --download-library bacteria --db $KDB |
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#!/usr/bin/env nextflow | |
params.testdir = "/cephfs/covid/software/sam/nf-test/" | |
params.fofn_single = [params.testdir, 'samples.csv'].join('/') | |
single_manifest_ch = Channel | |
.fromPath(params.fofn_single) // open say, a CSV | |
.splitCsv(header:true) // split text stream into CSV records | |
.map { row-> file(row.path) } // coerce the record and return a file for each line | |
.collect() // emit all items as one |
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#!/usr/bin/env python3 | |
import sys | |
import subprocess | |
p = subprocess.Popen("git ls-files --others --exclude-standard", shell=True, stdout=subprocess.PIPE) | |
out, err = p.communicate() | |
migrations = [] | |
for unchecked_rp in out.decode('UTF-8').split('\n'): | |
if "migrations" in unchecked_rp: |