1231 days ago
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has more (1200?), but they require you to sign up import reques...1150 days ago
2278 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
..._to_ctg_map.py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in one go. An example call for mapping with this script is python reads_to_ctg_map.py /path/to/...2138 days ago
2151 days ago
Install Python locally on shared Linux server !
#Install python to local directory #Firstly,...home directory, download the python source and extract it mkdir ~/python cd ~/python wget http...p. By the default, if we type python command, it will use the defa...k, run this command: which python #it should show you the path...2112 days ago
Installing pb-assembly on Linux !
...016a BLAST+/2.3.0-foss-2016a-Python-2.7.11...numpy/1.6.2-goolf-1.4.10-Python-2.7.3 fftw3/gcc/64/3.1.2...Python/2.7.3-goolf-1.4.10 goalf/1.1...a237_0 bioconda python-sortedcontainers: 2.0.4-py_0...2048 days ago
Installing Platypus on Ubuntu !
...Preparing to unpack .../0-libpython3.6_3.6.6-1~18.04_amd64.deb .....Downloading https://files.pythonhosted.org/packages/85/29/ccdb...e/anaconda3/envs/py27/include/python2.7 -c cython/cerrormodel.c -o...rbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-...2033 days ago
Setting up falconUnzip conda environments for genome assembly !
...622 KB conda-forge avro-python2-1.8.2 |...964 KB conda-forge python-edlib-1.2.3.post1 | py27h...conda-forge avro-python2: 1.8.2-py_1...bioconda python-edlib: 1.2.3.post1...2004 days ago
Backward Elimination with Python
#Backward Elimination with p-values only: import statsmodels.formula.api as sm def backwardElimination(x, sl): numVars = len(x[0]) for i in range(0, numVa...1969 days ago