Coding4Medicine-2017

Programs written for teaching Coding4Medicine 2017

File descriptions:

• states.py: Converts state abbreviations into full names
  • states.txt: Data used in dictionary
• aldh.py: Converts a string of nucleotides into amino acids
  • genetic-code.txt: Data used in dictionary
  • ALDH.txt: Input gene
  • random-gene.txt: Input gene
  • protein.txt: Output protein
• random-gene.py: Generates a random string of nucleotides to demonstrate DNA is not random (too many stop codons)
  • random-gene.txt: Output file
• biopython.py: A test program used for messing with the Biopython library
• cointoss.py: Determines when a person tossing a coin has changed to a coin with different weights
• n50.py: Calculates N50 value to score DNA sequence quality
• n90.py: Calculates N90 value to score DNA sequence quality
• tables.py: Says who sits with who
• Compare-Human-Chimp/: Used for an experiment comparing human genes with chimp genes
  • MC1R.fa: Input gene for human and chimp (the chimp one doesn't match exactly, since I extracted it from a different genome)
  • MC1R.aln: Human and chimp MC1R genes aligned
  • pull.py: Pulls a certain gene from a genome (used BLAST to find the human one in chimp, then extracted it with this to align them)
• Ancestry/: Used for an experiment for sorting people by race by their genomes
  • categorize.py: Groups people by their race by using their genomes
  • person[1-5]: 5 slightly modified versions of south-america
  • random-edit.py: Makes user-specified random edits to an input genome
  • south-america/asia/africa/europe: Fake auto-generated genomes
• Jigsaw/: Used for assembling a genome from pieces
  • debruijn.py: Uses a Debruijn graph to assemble gene fragments
    • puzzle-out.txt: Output from debruijn.py
  • check.py: Makes sure output from debruijn.py is correct
  • puzzle.csv/puzzle2.csv/nucl-puzzle.txt: Fragmented genes
  • Kmer-Exercises/: Smaller scripts for working with k-mers
    • k-mers.py: Counts the k-mers of a genome
      • k-mers.txt: Number of 35-mers in E.coli K12 genome
    • length.py: Prints the length of a genome
    • random-gene.fa: Random gene of about equal length to E. coli K12 genome
    • ALDH.fa: Same as /ALDH.txt but FASTA format, for testing with k-mers.py