Tutorial-1 : How to run the transposonmapper python package in a specific environment.¶
Installing python package for users¶
git clone https://github.com/SATAY-LL/Transposonmapper.git Transposonmapper
cd Transposonmapper
conda env create --file conda/environment.yml
conda activate satay
pip install -e .
Installing python package for developers¶
git clone https://github.com/SATAY-LL/Transposonmapper.git Transposonmapper
cd Transposonmapper
conda env create --file conda/environment-dev.yml
conda activate satay-dev
pip install -e .[dev]
Importing the required python libraries¶
import os, sys
import warnings
import timeit
import numpy as np
import pysam
import pandas as pd
# importing the transposon mapping function
from transposonmapper import transposonmapper
Invoking the transposonmapper package with a dummy file¶
bamfile= '../transposonmapper/data_files/files4test/SRR062634.filt_trimmed.sorted.bam'
filename='SRR062634.filt_trimmed.sorted.bam'
assert os.path.isfile(bamfile), "Not a file or directoy"
transposonmapper(bamfile=bamfile)