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CSBiology / BioFSharp

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Add pretty printers for common biological file formats

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kMutagene
kMutagene commented Dec 1, 2018

As analyzing biological data with BioFSharp involves a lot of scripting, optional pretty printers help a lot when looking at results directly in the fsi window. This should be especially easy to add for parsing libraries that can already write the correct file format. A basic pretty printer for biocollections is already impelemented.
Here are some formats from the top of my head, feel free to add

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up-for-grabs project-all good first issue

PetePrattis / chromosome-last-nucleotide-game

Star 1

A Python script that implements a two player strategic game with two chromosomes having length n and m of nucleotides respectively. In each Round of the game a player can destroy one of the chromosomes and split the other into two non-empty parts. The player who deletes the last nucleotide wins.

game python computer-science bioinformatics loop student arrays fasta program nucleotides chromosomes
  • Updated Nov 21, 2019
  • Python

PetePrattis / chromosome-last-random-nucleotide-game

Star 1

A Python script that implements a two player strategic game with two sequences of length n and m nucleotides respectively. At each Round of the game a player can remove a random number of nucleotides from one sequence or the same number of nucleotides from both sequences. The player who removes the last nucleotide wins.

game python computer-science bioinformatics loop student arrays fasta program nucleotides chromosomes
  • Updated Nov 22, 2019
  • Python

PetePrattis / Chimeric-Alignment-problem

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A python script that implements an efficient algorithm for the Chimeric Alignment problem. A virus infects a bacterium and modifies a replication process in the bacterium by adding for each A an A sequence of length 1-5, for each C a C sequence of length 1-10, for each G a G sequence of length >= 1 and for each T a T sequence of length >= 1.

python computer-science bioinformatics student sequence program nucleotides chromosomes chimeric-alignment
  • Updated Nov 26, 2019
  • Python

PetePrattis / sequence-global-alignment-with-unknown-nucleotides

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A Python script that for a parameter k, calculates the universal alignment of 2 sequences, with limitation that the alignment contains at most k unknown nucleotides. Nucleotide sequences are sometimes written in a 5-character alphabet, A, T, G, C, and N where N stands for an undefined nucleotide.

python computer-science bioinformatics student fasta program global-alignment sequence-alignment nucleotides chromosomes
  • Updated Nov 25, 2019
  • Python

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