Labs completed for Research Programming in the Life Sciences 2022. Written in OOP.

Assignments and python programs:

• Manipulating Data Types

  • seqCleaner: Removes ambiguous base (“N”) output from a sequencer.
  • fastqParse: Parses FASTQ sequence file and collects instrument, run ID, flow cell ID, flow cell lane, tile number, and coordinate information.
  • coordinateMathSoln: Building off a premade class, calculates the bond lengths and angles of three sets of atomic coordinates provided in one line.
  • converter: Using dictionary mappings, converts RNA and DNA codons to amino acid symbols.

• ProteinParam

  • Calculates the physical-chemical properties of an input protein sequence. Outputs molecular weight, molar extinction coefficient, mass extinction coefficient, theoretical pI, and amino acid composition (in %).

• sequenceAnalysis

  • NucParams: Calculates codon, amino acid, and nucleotide counts for an input nucleotide sequence.
  • addSequence: Accepts additional sequences from input for analysis.
  • aaComposition: Counts number of amino acids in nucleotide sequence.
  • codonComposition: Counts the number times a valid amino acid codon appears in the nucleotide sequence.
  • Calls on ProteinParam class to output additional information about predicted protein.\
  • GenomeAnalyzer.py: Imports sequenceAnalysis module and prints out statistical values of codons, nucleic acids, and amino acids.