mer-freq

Dependencies

• Python 2.7.+
• Biopython 1.68+
• NumPy
• Pandas
• regex
• SciPy

Database

• Merge split compressed files into single text file: cd db && cat 4mer_MCM.Bacteria.RefSeq.json.gz.0* | gunzip -c > 4mer_MCM.Bacteria.RefSeq.json
• Convert json into pkl because it's about 5 sec instead of 12 sec to load: json2pickle.py 4mer_MCM.Bacteria.RefSeq.json 4mer_MCM.Bacteria.RefSeq.pkl

Run example

• Query local genomes of interest against RefSeq: mer-freq --in-pkl ~/mer-freq/db/4mer_MCM.Bacteria.RefSeq.pkl --r-intra-sets --r-inter-db-sets --asm-acc filenames --min-correlation 0.9 -m fasta */*.fna.gz 1> 4mer-freq.assems_against_RefSeq.tsv 2> 4mer-freq.asm.err