Results for "Python Training"
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.1205 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...1125 days ago
A multilayer perceptron (MLP) neural network in Perl
#!/usr/local/bin/perl -w #################################################### #ML...near output neuron #To include an input bias create an #extra input in the training data #and set to 1 ####...2904 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
2253 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...2113 days ago
- #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin ex...me/urbe/Tools/augustus-3.2.3/config #run BUSCO python BUSCO.py -i /media/urbe/MyDDr...GRAALHaploid_BUSCO -m genome -f #Plot BUSCO python B...
2126 days ago
Install Python locally on shared Linux server !
...home directory, download the python source and extract it mkdir ~/python cd ~/python wget http...xfv Python-2.7.11.tgz find ~/python -type d | xargs chmod 0755 c...p. By the default, if we type python command, it will use the defa...k, run this command: which python...2087 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ 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...2023 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...2008 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environmen...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...1978 days ago
