Category / Python

by bioinfocore

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['font.family'] = '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.xticks(fontname='Arial')
plt.yticks(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'))

Source:
https://jonathansoma.com/lede/data-studio/matplotlib/exporting-from-matplotlib-to-open-in-adobe-illustrator/
https://stackoverflow.com/questions/20753782/default-fonts-in-seaborn-statistical-data-visualization-in-ipython
https://stackoverflow.com/questions/47112522/matplotlib-how-to-set-legends-font-type
https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html

by bioinfocore

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.
yourVar

To list and delete the stored variable:

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

Source:
https://stackoverflow.com/questions/35935670/share-variables-between-different-jupyter-notebooks
https://ipython.org/ipython-doc/rel-0.12/config/extensions/storemagic.html

by bioinfocore

Ignore row with only NaN in plotHeatmap – deepTools

If there are NaN in the output from computeMatrix, the generated heatmap is not sorted and a warning message stating Mean of empty slice will show up.

To overcome this, those null values need to be replaced using 0 in the computeMatrix step by --missingDataAsZero tag.

computeMatrix scale-regions -S xxx.bw -R xxx.bed --missingDataAsZero -m xxx -b xxx -a xxx --numberOfProcessors xx -o xxx.gz

plotHeatmap -m xxx.gz -out xxx.png

Source:
https://groups.google.com/g/deeptools/c/B55e0kT_0Ec?pli=1
https://github.com/deeptools/deepTools/issues/490

by bioinfocore

Python return os.system and subprocess output as a string

When we want to use Unix command in python we can directly use os.system() to realize it. However, if we only want to return the output as a string, for example, return ls file names into a string, we need to use subprocess.check_out instead.

To note that, the output from subprocess.check_out() is a bytes object instead of a string, thus we need to further decode to transform into a string.

fileList = subprocess.check_output('ls someFolder/*', shell=True).decode('utf-8').strip().split('\n')

Source:
https://stackoverflow.com/questions/606191/convert-bytes-to-a-string

by bioinfocore

Extract/subset bigwig file for a given genomic region

This is a solution in python version (3.0+) using a package called pyBigWig to extract a given genomic region from a whole genome bigwig file.

Prepare your input bigwig file:

import pyBigWig

# First open bigwig file
bwIn = pyBigWig.open('input.bw')

# check bigwig file header
print(bwIn.header())

Prepare output, since your output doesn’t have a header, you need to add the header using the chosen chromosome size, here I’m using a region from chr18 as an example.

bwOutput = pyBigWig.open('output.bw','w')
bwOutput.addHeader([('chr18',80373285)]) # chromosome size

for x in bwIn.intervals('chr18',62926563,63516911):
    bwOutput.addEntries(['chr18'],[x[0]],ends=[x[1]],values=[x[2]])

bwOutput.close()