A protein sequence fetching and database-building tool

Currently optimized to work with IAV subtypes and their respective protein sequences. Certain functions may not work accurately for other organisms.

The PRDB (Protein Retrieval Database) program is designed to fetch protein sequences of Influenza A Virus (IAV) from the NCBI database using taxonomic IDs. This manual provides instructions on how to use the program effectively.

• Python 3.x
• Biopython library (install using pip install biopython)

python prdb.py [-h] (--email EMAIL{STR}) (--txid TXID [TXID ...][INT]) [--db DB [DB ...]{STR}] 
    [--sub SUB [SUB ...]{STR}] [--gene GENE [GENE ...]{STR}] [--min MIN][INT] [--max MAX][INT] 
    [--meta <filename>]{STR} [--F <filename>]{STR}

• -h: Show the help message and exit.
• --email: Your email ID to access the NCBI database. Required.
• --txid: Taxonomic ID of the organism(s) of interest. Can provide multiple IDs. Required.
• --db: Search specific database(s). Can provide multiple database names.
• --sub: Search for specific subtypes. Can provide multiple subtype names.
• --gene: Search for specific gene(s) encoding the desired protein(s). Can provide multiple gene names.
• --min: Threshold for the minimum length of the sequence.
• --max: Threshold for the maximum length of the sequence.
• --full: Only search for complete sequences.
• --meta: Output filename to store the metadata for the sequences found.
• --F: Output filename to store the sequences found.

1. Provide Your Email: Start by entering your email ID using the --email option. This is necessary to access the NCBI database.

2. Taxonomic IDs (txid): Use the --txid option to specify the taxonomic IDs of the organisms you want to search for. You can provide multiple IDs separated by spaces. ** Use 11320 for IAV viral proteomes. It is required to input the taxonomical ID to initiate the search.

3. Search Criteria:

   • Database (db): If you want to search in specific databases, use the --db option and provide one or more database names. e.g. genbank, refseq or swissprot.
   • Subtype (sub): Use the --sub option to search for specific subtypes. Provide subtype names.
   • Gene Name (gene): To search for sequences associated with specific gene names, use the --gene option and provide gene names.

4. Sequence Length Criteria:

   • Minimum Length (min): Use the --min option to specify the minimum sequence length.
   • Maximum Length (max): Use the --max option to specify the maximum sequence length.

5. Complete Sequences Only: If you're interested in complete sequences only, use the --full flag.

6. Output Files:

   • Sequences File (--F): To save the searched protein sequences, use the --F option followed by the desired output filename. It outputs a fasta file.
   • Metadata File (--meta): To save associated metadata, use the --meta option followed by the desired output filename. It outputs a CSV file.

1. Fetch protein sequences of Influenza A Virus subtype H1N1 from taxonomic ID 11320:

   python prdb.py --email [email protected] --txid 11320 --sub H1N1 --F sequences_output
   

2. Fetch sequences from taxonomic IDs 11320, search for subtype H1N1 and H3N2, and save metadata:

   python prdb.py --email [email protected] --txid 11320 --sub H1N1 H3N2 --meta metadata_output