Laboratory on SQLite in Python!

Introduction

The GPM is an experimental project to create knowledge from proteomics data & reuse it solve biomedical research problems.

• Download the database from the server: http://www.cs.mcgill.ca/~mperre12/static/GPM.gpmdb

Analyzing the GPM database in Python!

• You can explore the structure of the database and try queries using the sqlite3 tool, but the following questions need to be answered in Python

• Your script should do the following:
  • Print the number of entries for which the expectation is greater than -100 in the "Protein" table.
  • Print the average length of a sequence in the Peptide table.

Making a copy and modifying it in Python!

• Make a copy of the database

• Congrats! You've discovered a new "thing" and it's the next best "thing". You decide to call it polyphenopeptobismols, and there's one of those for each Peptide id.
  • Create new table called polyphenopeptobismols with a pid (peptide id) as the primary key, and a column awesomeness that will be populated in the next step with a number from 0 to 100.
  • For each peptide in the Peptide table, add a record in your new table polyphenopeptobismols that uses the peptide id as the primary key, and a random value from 0 to 100 in the awesomeness column (Google how to get a random integer from the "random" module in python)