Humaasif

import matplotlib.pyplot as plt

# Setup arrays to store train and test accuracies
neighbors = np.arange(1, 9)
train_accuracy = np.empty(len(neighbors))
test_accuracy = np.empty(len(neighbors))

# Loop over different values of k
for i, k in enumerate(neighbors):
    # Setup a k-NN Classifier with k neighbors: knn

Humaasif

# Download Kallisto and sratools (the latter to be able to download from SRA)
wget https://github.com/pachterlab/kallisto/releases/download/v0.42.3/kallisto_mac-v0.42.3.tar.gz
tar zvxf kallisto_mac-v0.42.3.tar.gz 
wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.5.2/sratoolkit.2.5.2-mac64.tar.gz
tar zxvf sratoolkit.2.5.2-mac64.tar.gz

# Download and merge human cDNA and ncDNA files from Ensembl for the index.
wget ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
wget ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz
cat Homo_sapiens.GRCh38.cdna.all.fa.gz Homo_sapiens.GRCh38.ncrna.fa.gz > Homo_sapiens.GRCh38.rna.fa.gz

Humaasif

%%writefile make_conda_env.sh
#!/usr/bin/env bash
# author: github.com/ruxi
# reproducibly create conda env

read -p "Create new conda env (y/n)?" CONT

if [ "$CONT" == "n" ]; then
  echo "exit";
else

Humaasif

%%writefile make_conda_env.sh
#!/usr/bin/env bash
# author: github.com/ruxi
# reproducibly create conda env

read -p "Create new conda env (y/n)?" CONT

if [ "$CONT" == "n" ]; then
  echo "exit";
else