文章目錄
Apri 19, 2019
1.How to know/change current directory in Python shell?
import os
os.getcwd() # know current directory
os.chdir("/tmp/") # change curren directory
2.How to use python virtual envirment?
sudo apt update
sudo apt install python3-dev python3-pip
sudo pip3 install -U virtualenv
virtualenv --system-site-packages -p python3 ./venv
source ./venv/bin/activate
deactivate
3.How to call external commands in Python script?
from subprocess import call
call(['prepare_ligand4.py', '-l {0} -o {1}/{2}.pdbqt -A checkhydrogens'.format("/tmp/ligand.mol2", library_PostPrepare_folder, mol_id)])
4.How to list all filenames and subdirectories of a directory?
os.listdir(path)
4.1 List only files:
from os import listdir
from os.path import isfile, join
onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]
import glob
mypath = "/home/zdx/Downloads/topoII/*"
print(glob.glob(mypath))
5.map
ligand_name = list(map(fun, var))
6.dataframe
from pandas import Series,DataFrame
import pandas as pd
data = {'state':ligand_name,'cnnscore':cnnscore}
df = DataFrame(data)
7.sort dataframe
df = df.sort_values(by='cnnscore', ascending=False)
8.output dataframe
df.to_csv(f_t, sep='\t', index=False, encoding='utf-8')
9.read excel and csv
df = pd.read_excel('topoII.true_label.xlsx', index_col=0)
df = pd.read_csv(score_file, header = None, names = ['label', 'score'])
10.locate values
df_t[df_t['label']==0].index.values.astype(int)
11.dataframe batch process
df['ID'] = df['ID'].apply(extract_number)
12.delete column from dataframe
del df['column_name']
13.index dataframe
df.iat[0,0]
14.shuffle dataframe
df = df.sample(frac=1).reset_index(drop=True) # dataframe shuffle