jodyphelan

gyrB	p.Arg446Cys	6575
gyrB	p.Arg446His	6576
gyrB	p.Arg446Leu	6576
gyrB	p.Ser447Phe	6579
gyrB	p.Asp461Asn	6620
gyrB	p.Asp461His	6620
gyrB	p.Asp461Ala	6621
gyrB	p.Gly470Cys	6647
gyrB	p.Ile486Leu	6695
gyrB	p.Asp494Ala	6720

jodyphelan

def get_barcode_performance(csv_file, tree_file, lineage):
    meta = []
    for row in csv.DictReader(open(args.csv)):
        meta.append(row)

    try:
        t = ete3.Tree(args.tree,format=1)
    except:
        t = ete3.Tree(args.tree)

jodyphelan

"""
I want to loop through a file that contains:
Rv0001  10
Rv0001  20
Rv0002  50
Rv0003  70

and I want something that looks like this:
{
    "Rv0001": [10,20],

jodyphelan

Biological_sample	Replicate + calling params	number of snps across replicates	num snps in run
por8	por8B_mq0_bq5	7	7
por8	por8A_mq60_bq0	7	7
por8	por8C_mq0_bq15	7	7
por8	por8B_mq10_bq5	7	7
por8	por8A_mq40_bq20	7	7
por8	por8C_mq30_bq15	7	7
por8	por8C_mq10_bq20	7	7
por8	por8A_mq30_bq0	7	7
por8	por8A_mq60_bq15	7	7

jodyphelan

import sys
import gzip
import os.path
import subprocess
from collections import defaultdict
import random
import argparse
rand_generator = random.SystemRandom()

jodyphelan

import sys
import argparse
import csv
import subprocess
from tqdm import tqdm
import gzip

def num_mismatches(str_x,str_y):
    mismatches = 0
    for char_x,char_y in zip(str_x,str_y):

jodyphelan

bcftools view -V indels merged.raw.vcf.gz | setGT.py | bcftools view -a | bcftools filter -e 'GT="het"' -S . | bcftools view -i 'F_PASS(GT!="mis")>0.9'  | bcftools view -c 1 | bcftools norm -f ../reference/Mycobacterium_abscessus.7396_7_44.dna.toplevel.fa | bcftools view -Oz -o merged.filt.vcf.gz

jodyphelan

test_env=testing
mamba create -y -n $test_env python bwa "samtools>=1.12" "bcftools>=1.12" requests snpEff jq samclip gatk4 trimmomatic parallel "delly>=1.1.7" "freebayes==1.3.6" tqdm minimap2 bedtools jinja2 samclip kmc pilon lofreq filelock mash docxtpl dsk pysam rich-argparse joblib  iqtree pydantic tomli itol-config sourmash
conda activate $test_env
pip install rich_argparse
mamba install flask celery redis sqlalchemy psycopg2
pip install redis flask_sqlalchemy flask_login flask_session flask_wtf email_validator
pip install --force-reinstall git+https://github.com/jodyphelan/TBProfiler.git@dev
pip install --force-reinstall git+https://github.com/jodyphelan/pathogen-profiler.git@dev

jodyphelan

bedtools genomecov -ibam bam/por1_fastq.bam -bga | awk '$4==0' | bedtools intersect -a - -b ~/miniconda3/envs/dev/share/tbprofiler/tbdb.bed | bedtools subtract -a - -b test2.vcf 

jodyphelan

sudo mount -o remount,size=26386392k tmpfs /run
sudo mount -o remount,size=40386396k tmpfs /run/user/506/