Pandas merge or sum values in rows with the same index

When the values are numeric and apply operators:


When the values are numeric and apply functions:

# Common usage, merging values
df[1].groupby(level=0).apply(lambda xList: ';'.join(list([x for x in xList])))


Python matplotlib: all about fonts

Fonts output into pdf as text, not shape, to be recognized in Illustrator:

import matplotlib
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fonttype'] = 42

Change fonts style for all, change the default:

import matplotlib as mpl
matplotlib.rcParams[''] = 'Arial'

Change fonts style for labels, tick marks, and titles: (for each plot, not changing the default)

plt.xlabel('XXXX', fontsize=12, fontname='Arial')
plt.ylabel('XXXXX', fontsize=12, fontname='Arial')


plt.title('XXXXX', fontsize=14, fontname='Arial')

Change legend font style: (for each plot, not changing the default)

plt.legend(prop=matplotlib.font_manager.FontProperties(family='Arial', size=12, weight='bold', style='normal'))


Liftover bam files

The most straightforward way is using CrossMap.

Taking from hg19 to hg38 as example:

pip install CrossMap bam -a hg19ToHg38.over.chain input.bam output
#.bam extension will be added automatically

genome liftover chain files can be downloaded here: (change according to your needs)

It is suggested to always use ‘-a’ option according to the CrossMap website.


Python Jupyter notebook share the variable across notebooks

yourVar = 'data or your variable'
%store yourVar
del yourVar # only deletes the variable in this notebook but not in store

In the second notebook:

%store -r yourVar # if you have a variable with the same name, it will rewrite it.

To list and delete the stored variable:

%store #list variable in store
%store -d yourVar #delete the variable in store