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Phage-NCBI-tails-data-cleaning

This little python script made my life easier when I had to clean up and extract data from the NCBI protein database for a biochemistry research project.

What it does

For each file in the raw_data directory, the script will:

  1. Filter the HMM (Name) by each protein family.
  2. Count the number of Prot RefSeqs for that family. Record this number as "Total #hits".
  3. Filter for E values less than 0.001 and count the Prot RefSeqs that satisfy this condition.
  4. Filter for unique Prot RefSeqs and record this number as "Unique hits".
  5. Generate a new file containing the totals hits, number of E values less than 0.001 and unique hits.
  6. Generate a new file containing the unique Prot RefSeqs and their smallest E values and protein family identity.
  7. Move on to the next file in the raw_data directory to repeat steps 1-6.