Problem to solve with this software:

• Plain fasta files are bad databases

First ideas:

• Database of genes for secondary bile-acid synthesis (avg. file size = KB's)
• TCGA downloads of cancer genes (avg. file size = 3GB uncompressed)
• Host genomes used for microbiome research (size depends on host)
• More organized KEGG ortholog database (whole peptide database = 4.3GB uncompressed)
• Urease genes (avg. file size = KB's)

What we want to feed into a database:

• Fasta file(s)
• File(s) of metadata (.json, .yaml, or something else)
• OR Sqlite database of metadata

What it might look like in the folder: my_folder _ my.fasta _ metadata.json OR _ metadata.db

Example commands:

• list_sequences [db_name] : spits out the names of sequences
• get_metadata [sequence_name] : gives you metadata for a given sequence
• import_db [fasta_file] [metadata_1] [metadata_2] : prepares the first iteration of the database, timestamps and gives info on where data was downloaded
• update_db [your_db] [other fasta file] [other metadata] : performs a union / updates your_db with new / updated sequences
• update_metadata [your_db] [sequence_name] [updated_data] : change a specific item of metadata
• summarize_db [your_db] : gives statistics like # of sequences, # of metadata items, data created, date downloaded, etc.

Tasks:

• Kyle will set up skeleton code for the python package
• Scott will get a few sequences and metadata for testing
• Brad will get started on metadata fields
• Vince will start with import_db function once skeleton and test sequences are in place