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

wget ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz
gunzip Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz
mv Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa H37Rv.fa
printf "Chromosome\t5\tX\tT\n" > snp.txt
printf "Chromosome\t50000\tX\tT\n" >> snp.txt
seqtk  mutfa H37Rv.fa snp.txt >mutant.fa

# My current command
minimap2 H37Rv.fa mutant.fa --cs | sort -k6,6 -k8,8 |  paftools.js call -l 100 -L 100 -f H37Rv.fa -s test - 

jodyphelan

TBProfiler report
=================

The following report has been generated by TBProfiler.

Summary
-------
ID: SRR6824414
Date: Mon Oct 12 17:33:42 2020
Strain: lineage4.5;lineage3

jodyphelan

###################
#### Create DB ####
###################

# This is just a simple in-memory sqlite database for this example.
# It will obviously not be necessary in your case as you already created the database.

from sqlalchemy import Table, Column, Integer, String, MetaData, ForeignKey
from sqlalchemy import create_engine

jodyphelan

import sys
import argparse
import re
import subprocess as sp


def main(args):
    IN = sys.stdin if args.vcf=="-" else sp.Popen("bcftools view %(vcf)s" % vars(args),shell=True,stdout=sp.PIPE).stdout
    for l in IN:
        try:

jodyphelan

name: tb-profiler-dev
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - attrs=21.2.0=pyhd8ed1ab_0
  - bcftools=1.12=h45bccc9_1

jodyphelan

# Use the yml file to create the tb-profiler conda env
wget https://gist.githubusercontent.com/jodyphelan/92ec9b18f5b929bd1637d56568abbd0a/raw/ae52641f56cfa982c0a2febade10b2b7b882b6fa/tb-profiler-env.yaml
conda env create -f tb-profiler-env.yaml

# Activate env
conda activate tb-profiler-dev

jodyphelan

Install latest tb-profiler

1. Use the yml file to create the tb-profiler conda env

wget https://gist.githubusercontent.com/jodyphelan/92ec9b18f5b929bd1637d56568abbd0a/raw/ae52641f56cfa982c0a2febade10b2b7b882b6fa/tb-profiler-env.yaml
conda env create -f tb-profiler-env.yaml

2. Activate env

 conda activate tb-profiler-dev

jodyphelan

import sys
import argparse
import csv

def main(args):
    with open(args.db) as IN:
        reader = csv.DictReader(IN,delimiter="\t")
        if args.debug:
            sys.stderr.write(str(reader.fieldnames)+"\n")
        for c in args.columns:

jodyphelan

# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-11.2.0-h5c6108e_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.1.0-ha89aaad_16.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/openjdk-8.0.302-h7f98852_0.tar.bz2