GitHub - robertoamarie/FMindexPy: A simple propedeutic Python script developed under the scope of an academic exam on Scientific Programming. Aimed at creating all the data structures of a FM index starting from a single FASTA file, and storing them in a desired target folder.

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A simple propedeutic Python script developed under the scope of an academic exam on Scientific Programming. Aimed at creating all the data structures of a FM index starting from a single FASTA file, and storing them in a desired target folder.

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Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
FMindex.sh		FMindex.sh
FMindexPy.py		FMindexPy.py
NC_000001_nonN_subset_100k.fa		NC_000001_nonN_subset_100k.fa
README		README
environment.yml		environment.yml

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The current folder provides:
> the FMindexPy.py script for creating all the data structures of a FM index starting from a single FASTA file, and storing them in a desired target folder. (For more details, consult the script itself)
> a FASTA file downloaded from the publicly available NCBI's Sequence Viewer (https://www.ncbi.nlm.nih.gov/projects/sviewer/)
> a subsetted version of the above FASTA file that meets the requirements of the FMindex.Py script 
> a YAML file to facilitate the download of the needed dependencies within a conda environment
> an example of a sbatch script that has been used during the development phase to run and test the script with the above mentioned dataset