Results for "Python%20versions"
Bio-Scripts
(JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1217 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 requ...1136 days ago
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2264 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 used to obtain such files. Read pairs needs to be aligned in...2124 days ago
- #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/scripts export AUGUSTUS_CONFIG_PATH...
2137 days ago
Install Python locally on shared Linux server !
#Install python to local directory #Firstly, I create a folder in my home directory, download the python source and extract it mkdir ~/python cd ~/python wget ht...2098 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail -------------------------------------------------------- /usr/share/Modules/modulefiles -----------------------------------------------...2034 days ago
Installing Platypus on Ubuntu !
(py27) ➜ Tools git:(master) ✗ git clone https://github.com/andyrimmer/Platypus.git Cloning into 'Platypus'... remote: Enumerating objects: 1394, done...2019 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/denovo_asm Proceed...1990 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, numVars):...1955 days ago
