NucParams class

$q,$ init $q,$

The constructor of the class has one optional parameter, a sequence of type string. It may include upper or lower case letters of the set $\{$ACGTUN$\}$ or whitespace. These will be gene sequences and they begin in frame $1.$ In other words the first $3$ letters of the sequence encode the first AA of the sequence. Carefully consider in what form this class should maintain its data. Is a string the best structure? This class $($NucParams$)$ is intended to be very similar to ProteinParam. Make sure to read addSequence$($ before making this decision, and remember that objects of this class may need to handle an arbitrarily large number of sequences $($hint: dictionaries are good$).$ As a second hint, notice that init and addSequence are doing VERY similar things $-$ you could just make one of them do most of the work.

addSequence$()-5$ pts

This method must accept new sequences, from the $\{$ACGTUN$\}$ alphabet, and each sequence can be presumed to start in frame $1.$ This data must be added to the data that you were given with the init method $($if any$).$

aaComposition$()-6$ pts

This method will return a dictionary of counts over the $20$ amino acids and stop codons. This dictionary is VERY similar to the lab $3$ aaComposition, though you must decode the codon first. The translation table from codon to AA is provided. You are counting amino acids by translating from the proper codon table.

nucComposition$()-10$ pts

This method returns a dictionary of counts of valid nucleotides found in the analysis. $($ACGTNU$).$ If you were given RNA nucleotides, they should be counted as RNA nucleotides. If you were given DNA nucleotides, they should be counted as DNA nucleotides. Any N bases found should be counted also. Invalid bases are to be ignored in this dictionary.

codonComposition$()-10$ pts

This dictionary returns counts of codons. Presume that sequences start in frame $1,$ accept the alphabet $\{$ACGTUN$\}$ and store codons in RNA format, along with their counts. Any codons found with invalid bases should be discarded. Discard codons that contain $N$ bases. This means that all codon counts are stored as RNA codons, even if the input happens to be DNA. If you discard a codon, make sure to not alter the frame of subsequent codons.