python.md

Python utilities

Drop columns only with 0's

df.loc[:, (df != 0).any(axis=0)]

Drop rows only with 0's

df.loc[~(df==0).all(axis=1)]

Remove index name

df = df.rename_axis(None, axis = 1)

Remove percentage

df[col] = df[col].str.rstrip('%').astype('float') / 100.0

Sum per row

df.loc[:,'Total'] = df.sum(numeric_only=True, axis=1)

Count positive values per:

# row
df["Counts"] = len(df.columns) - df.apply(lambda row: sum(row[0:]==0) ,axis=1)
# column
df.loc["Counts",:] = len(df.index) - df.apply(lambda column: sum(column[0:]==0) ,axis=0)

Change display number of rows or columns:

pd.set_option('display.max_rows', 1000)
pd.set_option('display.max_columns', 1000)

to remove SettingWithCopyWarning:

pd.set_option('mode.chained_assignment', None)

To remove possible whitespaces (tabs) on the dataframe:

df = df.apply(lambda x: x.str.strip() if x.dtype == "object" else x)

Print column names:

cols = df.columns.tolist()
print(cols)

cols = list(df.columns)
print('", "'.join(cols))

Statistics

statistics = df.describe().loc[["mean", "std", "min", "25%", "50%", "75%", "max"]].round(2)

get current directory

import os
os.getcwd()

change directory

os.chdir("/path/")

basic file creation

with open(args.taxonomy, "r+") as f:
    lines = f.readlines()
f.close()

append to dictionary

if x not in d.keys():
    d[x] = y
elif x in d.keys():
    d[x].append(y)

---

Script with pass arguments

import argparse
parser = argparse.ArgumentParser(description='Move bins according to taxonomy')
parser.add_argument("taxonomy", help="File with gtdb result")
args = parser.parse_args()
print("\n")
print("Using:")
print("~ Taxonomy: {}".format(args.taxonomy))