bioinformatics_HIAE

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Implementation of HIAE challenge | question 5.

Problem Definition

Given n DNA strings whose size does not exceed 1000 bases, and that from these n reads it is possible to build an entire chromosome by aligning pairs of reads that overlap more than half their size, the goal is to return the superstring of smallest possible dimension containing all strings (this is equivalent in this problem to being able to reconstruct a chromosome).

Input EXAMPLE (input.txt):

• ATTAGACCTG
• CCTGCCGGAA
• AGACCTGCCG
• GCCGGAATAC

Output EXAMPLE (output.txt):

• ATTAGACCTGCCGGAATAC

Write a script in a language of your choice to receive an input.txt file and the output will be an output.txt file containing the superstring.

Usage

Warning: This solution was coded using Python 3,

To run the script, you first need to install the requirements:

pip install -r requirements.txt

Then, simple run:

python simple_aligner [input_file]

A file named output.txt will be created in the current directory containing the resulting chromosome.

Tests

To run the test suite, simple run:

pytest -v .