You are to extract and translate several genes with defined coordinates from their chromosome sequences. If you are applying for a position, it is highly recommended to complete the challenge in Python.
Three input files have been provided:
sequences.fastaA FASTA file with two chromosome sequences.intervals.gffA GFF file with a set of mRNA coordinates for the sequences insequences.fasta.standard_code.txtA tab delimited table mapping codons to single letter amino acids.
Using these three files, write a non-interactive command line tool that:
- Takes the three files as arguments,
- Extracts the mRNA sequences from
sequences.fastagiven the coordinates inintervals.gff, - Translates all six reading frames of the mRNA sequence given the genetic code in
standard_code.txt, - Prints the longest translation of each mRNA sequence to standard output in FASTA file format.
When evaluating the code, special attention will be given to the use of clean coding practices, maintainability and extensibility without over-engineering. The output for the given input files can be found in genes.fasta. Your solution will also be tested on additional input.