Here is a quick Python trick you might use in your code.
Most of the time, when you need to work on large data, you’ll have to use some dictionaries in Python. Dictionaries of lists are very useful to store large data in very organized way. You can always initiate them by initiating empty lists inside an empty dictionary but when you don’t know how many of them you’ll end up with and if you want an easier option, use
defaultdict(list). You just need to import it, first:
When you append a list to a list by using append() method, you’ll see your list is going to be appended as a list:
This post describes data preprocessing in Salmonella project for Prize-Collecting Steiner Forest Problem (PCSF) algorithm.
This task was given to me as a homework in one of my courses at the university and I wanted to share my solution as I saw there is no such entry on the Internet.
openpyxl is a Python library to read/write Excel 2007 xlsx/xlsm files. To download and install on Windows:
Numpy (Numerical Python) is a great Python package that you should definitely make use of if you’re doing scientific computing
So in our Multi-dimensional Modeling and Reconstruction of Signaling Networks in Salmonella-infected Human Cells project, we have several methods to construct the networks so the data is still needed to be preprocessed so that it can be ready to be analyzed with these methods.
You may need the conversion of PED files to FASTA format in your studies for further analyses. Use below script for this purpose.