Add and Subtract methods

[Adamtaranto]

New methods .add() and .subtract() to modify records in a KmerCountTable using a second table.

Create some new tables with different kmers and counts.

from oxli import KmerCountTable

# Create two KmerCountTable objects
kmer_table1 = KmerCountTable(ksize=3)
kmer_table2 = KmerCountTable(ksize=3)

# Count some k-mers
kmer_table1.count('AAA')
kmer_table1.count('TTT')
kmer_table1.count('AAC')

# Count for table 2
kmer_table2.count('AAA')
kmer_table2.count('AAG')

Check the table contents:

# Check the hashes for our kmers
print(f" Hash of 'AAA': {kmer_table1.hash_kmer('AAA')}") # 10679328328772601858
print(f" Hash of 'TTT': {kmer_table1.hash_kmer('TTT')}") # 10679328328772601858
print(f" Hash of 'AAC': {kmer_table1.hash_kmer('AAC')}") # 6579496673972597301
print(f" Hash of 'AAG': {kmer_table2.hash_kmer('AAG')}") # 12774992397053849803

# Check the hashes in each table
print(f"{kmer_table1.hashes}") # [10679328328772601858, 6579496673972597301]
print(f"{kmer_table2.hashes}") # [10679328328772601858, 12774992397053849803]

# List kmers and counts
list(kmer_table1) # [(10679328328772601858, 2), (6579496673972597301, 1)]
list(kmer_table2) # [(12774992397053849803, 1), (10679328328772601858, 1)]

Proposed behaviour for add():

• Check for same k, error if diff
• If hash is in both tables, combine values in self table
• If hash is only in non-self table, add new key to self + update count
• Non-self table is unchanged

# Add table 2 to table 1.
kmer_table1.add(kmer_table2)

list(kmer_table1) # [(10679328328772601858, 3), (6579496673972597301, 1), (12774992397053849803, 1)]

Proposed behaviour for subtract():

• Check for same k, error if diff
• If hash key is in both tables, substract non-self from self table.
• Any negative numbers after subtract should default to zero
• If value is zero after subtract then keep the key in self but set value to zero
• If hash only in non self table, do nothing, do not add key to self with value zero

# fresh KmerCountTable objects
kmer_table1 = KmerCountTable(ksize=3)
kmer_table2 = KmerCountTable(ksize=3)

# Count some k-mers
kmer_table1.count('AAA')
kmer_table1.count('TTT')
kmer_table1.count('AAC')

# Count for table 2
kmer_table2.count('AAA')
kmer_table2.count('AAG')

# List kmers and counts
list(kmer_table1) # [(10679328328772601858, 2), (6579496673972597301, 1)]
list(kmer_table2) # [(12774992397053849803, 1), (10679328328772601858, 1)]

# Subtract table 2 from table 1.
kmer_table1.subtract(kmer_table2)

# Inspect changes 
list(kmer_table1) # [(10679328328772601858, 1), (6579496673972597301, 1)] # AAA/TTT count reduced by 1

@ctb thoughts on subtract behaviour?

Could also add __add__ and __sub__ dunder methods to support things like kmer_table1 + kmer_table2. Though that might be confusing re which table is being updated, so maybe not.

Would we ever want to apply a constant to all values in a table? i.e. table + 1, table * 10, table - 1. If so that is probably a better use for the dunders.