1201 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...1120 days ago
2248 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be use...mem or BWA-sampe in one go. An example call for mapping with this script is python r...2108 days ago
2121 days ago
Install Python locally on shared Linux server !
...home directory, download the python source and extract it mkdir ~/python cd ~/python wget http...xfv Python-2.7.11.tgz find ~/python -type d | xargs chmod 0755 c...p. By the default, if we type python command, it will use the defa...k, run this command: which python...2082 days ago
Installing pb-assembly on Linux !
...Python/2.7.3-goolf-1.4.10 goalf/1.1...a237_0 bioconda python-sortedcontainers: 2.0.4-py_0...via Bioconda are: pre-release versions, not # # necessarily ISO...via Bioconda are: pre-release versions, not # # necessarily ISO...2018 days ago
Installing Platypus on Ubuntu !
...bionic-updates/main amd64 libpython3.6 amd64 3.6.6-1~18.04 [1.420...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...2003 days ago
Setting up falconUnzip conda environments for genome assembly !
...conda-forge avro-python2: 1.8.2-py_1...bioconda python-edlib: 1.2.3.post1...via Bioconda are: pre-release versions, not # # necessarily ISO...via Bioconda are: pre-release versions, not # # necessarily ISO...1974 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, numVar...1939 days ago