1180 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...1099 days ago
2227 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...2087 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict; use Carp; us...te', 'fallback' => 'TRUE'; # These methods should be overriden by child classes # class constructor sub new...2144 days ago
2100 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...2061 days ago
2038 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail ----------------------------...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...1997 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...1982 days ago