SamStudio8

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

SamStudio8

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",

SamStudio8

# 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/

SamStudio8

# 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;

SamStudio8

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"])

SamStudio8

PATH=$PATH:/home/ubuntu/ware/blast/ncbi-blast-2.7.1+/bin; 
kraken2-build --download-taxonomy --threads 24 --db /working/databases/kraken2-test/
kraken2-build --download-library archaea --db /working/databases/kraken2-test/
kraken2-build --download-library bacteria --db /working/databases/kraken2-test/
kraken2-build --download-library fungi --db /working/databases/kraken2-test/
kraken2-build --download-library protozoa --db /working/databases/kraken2-test/
kraken2-build --download-library viral --db /working/databases/kraken2-test/
kraken2-build --download-library UniVec_Core --db /working/databases/kraken2-test/
kraken2-build --threads 24 --build --db /working/databases/kraken2-test/

SamStudio8

import fitbit
import gather_keys_oauth2 as Oauth2
import datetime

CLIENT_ID =     'YOUR CLIENT'
CLIENT_SECRET = 'YOUR SECRET'

server = Oauth2.OAuth2Server(CLIENT_ID, CLIENT_SECRET)
server.browser_authorize()
ACCESS_TOKEN = str(server.fitbit.client.session.token['access_token'])

SamStudio8

y3 = [86,90,90,68,86,79,79,78,61,62,45,60]
y2 = [81,81,79,79,77,73,55,55,86,84,83,81]

# 8 modules per band
BAND_SIZE = 8
BAND_DELTA = len(y3) - BAND_SIZE

# Extract BAND_SIZE best year 3 modules
y3_sorted = sorted(y3)
band_3 = y3_sorted[-BAND_SIZE:]

SamStudio8

"""
A scrappy esoteric glue program for Ben because he only really likes databases.
Given a tab delimited file where:
    fields[0]  ORF id
    fields[1]  1-pos Start
    fields[2]  1-pos End
    fields[-1] Structural Prediction Code
Output a cast dataframe with a line per ORF, describing all structural predictions
for that ORF as a single string. Additionally enumerating each viable code's proportion
of that string as a percentage. You may alter CODES to add/remove prediction codes

SamStudio8

Program received signal SIGSEGV, Segmentation fault.
_int_malloc (av=av@entry=0x7ffff7dd6b40 <main_arena>, bytes=bytes@entry=24) at malloc.c:3803
3803              set_head (remainder, remainder_size | PREV_INUSE);
(gdb) bt
#0  _int_malloc (av=av@entry=0x7ffff7dd6b40 <main_arena>, bytes=bytes@entry=24) at malloc.c:3803
#1  0x00007ffff7a9e950 in __GI___libc_malloc (bytes=24) at malloc.c:2914
#2  0x0000000000400812 in main ()