Parsing and Converting workshop

BLAST report

• Ecoli proteins
• S_enterica proteins
• Ecoli-vs-Senterica.BLASTP.tab.gz

Write script to read in the BLAST report.

• Calculate for each alignment what the % aligned of the Ecoli query protein is?
• Calculate the % of proteome that was aligned (out of the total number of Ecoli proteins)

Parsing BLAST: https://github.com/biodataprog/GEN220_2019_examples/blob/master/Bioinformatics_2/parse_blast.py

Orthofinder parsing

Here is a data file - OrthoFinder result

• Let’s write a script which will summarize the data by Species.

The data look like

ORTHOGROUP	GENENAME_SP1, GENENAME2_SP1	GENENAME_SP2