jodyphelan

#! /usr/bin/env python
import argparse
import sys
import subprocess as sp
from tqdm import tqdm

def main(args):
    background = []
    foreground = []
    for l in tqdm(open(args.meta)):

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

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

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

# 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

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

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

###################
#### 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

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

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 -