python - One object in class overwriting the other -

i wrote module contains class methods return various information given dna sequence. want write module class can compare information 2 sequences. here have.

import genomeanalyzer g  class genomepair:      def __init__(self, gene_1, gene_2):             self.gene_1 = g.genome(gene_1)             self.gene_2 = g.genome(gene_2)      def comparegc(self):             print(self.gene_1.gccomp())             print(self.gene_2.gccomp())    genomepair_obj = genomepair("testtiny.fa", "halovolc1_1-genes.fa") genomepair_obj.comparegc() 

and here snippet of genome class uses module.

import sequenceanalysis seq   class genome:      def __init__(self, file):         """         separates sequence data header data in given fasta file,         creates nucparams object , calls codoncomposition method         populate codon dictionary.                """         self.file = file         self.fasta = seq.fastareader(self.file)         sequence = ""         pair in self.fasta.readfasta():              dna = pair[1]             sequence += dna         self.sequence = sequence         self.dna_obj = seq.nucparams(self.sequence)         seq.nucparams.codoncomposition(self) #necessary?      def gccomp(self):         sum = seq.nucparams.nuccount(self)         gc_count = 0         nuc in ['g', 'c']:             gc_count += seq.nucparams.nuc_freq[nuc]         gc_comp = ((gc_count / sum) * 100)         return gc_comp  

and nucparams:

class nucparams:      rnacodontable = {     # rna codon table     # u     'uuu': 'f', 'ucu': 's', 'uau': 'y', 'ugu': 'c', # uxu     'uuc': 'f', 'ucc': 's', 'uac': 'y', 'ugc': 'c', # uxc     'uua': 'l', 'uca': 's', 'uaa': '-', 'uga': '-', # uxa     'uug': 'l', 'ucg': 's', 'uag': '-', 'ugg': 'w', # uxg     # c     'cuu': 'l', 'ccu': 'p', 'cau': 'h', 'cgu': 'r', # cxu     'cuc': 'l', 'ccc': 'p', 'cac': 'h', 'cgc': 'r', # cxc     'cua': 'l', 'cca': 'p', 'caa': 'q', 'cga': 'r', # cxa     'cug': 'l', 'ccg': 'p', 'cag': 'q', 'cgg': 'r', # cxg     #     'auu': 'i', 'acu': 't', 'aau': 'n', 'agu': 's', # axu     'auc': 'i', 'acc': 't', 'aac': 'n', 'agc': 's', # axc     'aua': 'i', 'aca': 't', 'aaa': 'k', 'aga': 'r', # axa     'aug': 'm', 'acg': 't', 'aag': 'k', 'agg': 'r', # axg     # g     'guu': 'v', 'gcu': 'a', 'gau': 'd', 'ggu': 'g', # gxu     'guc': 'v', 'gcc': 'a', 'gac': 'd', 'ggc': 'g', # gxc     'gua': 'v', 'gca': 'a', 'gaa': 'e', 'gga': 'g', # gxa     'gug': 'v', 'gcg': 'a', 'gag': 'e', 'ggg': 'g'  # gxg     }     dnacodontable = {key.replace('u','t'):value key, value in rnacodontable.items()}     dna_codon_freq = {}     rna_codon_freq = {}     nuc_freq = {'a':0, 't':0, 'g':0, 'c':0, 'u':0, 'n':0}     aa_dic = {}     is_dna = true      def __init__ (self, sequence):         in nucparams.dnacodontable:              nucparams.dna_codon_freq[i] = 0         in nucparams.rnacodontable:             nucparams.rna_codon_freq[i] = 0         self.sequence = sequence         nucparams.addsequence(self,self.sequence)      def addsequence (self, thissequence):         s = ''.join(thissequence).split()         s = ''.join(s).upper()         clean_seq = ""         if 'u' in s:             nucparams.is_dna = false         nuc in s:             if nuc in ['a', 't', 'g', 'c', 'u', 'n']:                 clean_seq += nuc                 nucparams.nuc_freq[nuc] += 1         self.nuc_string = clean_seq         start, stop = 0, 3         codon_count = len(self.nuc_string) // 3         in range(codon_count):             codon = self.nuc_string[start:stop]             if 'n' in codon:                 pass             elif nucparams.is_dna == true:                 nucparams.dna_codon_freq[codon] += 1             elif nucparams.is_dna == false:                 nucparams.rna_codon_freq[codon] += 1             start += 3             stop += 3      def aacomposition(self):         if nucparams.is_dna:             freq = nucparams.dna_codon_freq             dic = nucparams.dnacodontable         else:             freq = nucparams.rna_codon_freq             dic = nucparams.rnacodontable         in dic:             x = dic.get(i)             nucparams.aa_dic[x] = 0         codon in freq:              nucparams.aa_dic[dic[codon]] += freq[codon]         return nucparams.aa_dic      def nuccomposition(self):         return nucparams.nuc_freq      def codoncomposition(self): #must output rna codon freq regardless of input         if nucparams.is_dna == false:             return nucparams.rna_codon_freq         else:             nucparams.rna_codon_freq = {key.replace('t','u'):value key, value in nucparams.dna_codon_freq.items()}             return nucparams.rna_codon_freq       def nuccount(self):         sum = 0         in nucparams.nuc_freq:             sum += nucparams.nuc_freq[i]         return sum 

the method gccomp() returns number 0-100 representing percentage of gs or cs in sequence.

when comment out self.gene_2 line in __init__ , corresponding print line prints gc comp of 50.0. when same self.gene_1 gc comp of 49.3. when both declared both hold value 49.3.

why when create second object overwrite first? have different names don't they?

there several possible problems concerning object oriented programming , difference between class , object variables.

e.g. in class seq.nucparams:

def nuccomposition(self):     return nucparams.nuc_freq 

this returning static (so class wide, in case program wide) value of nuc_freq - not nuc_freq of object (which self.nuc_freq).

another example:

in genome.__init__ assign self.dna_obj nucparams instance:

self.dna_obj = seq.nucparams(self.sequence) 

but won't use anymore in rest of code. seems you're using seq.nucparams class static functions instead of object methods.

i assume in gccomp() have use

sum = self.dna_obj.nuccount()       # instead of sum = seq.nucparams.nuccount(self) 

and

gc_count += self.dna_obj.nuc_freq[nuc]     # instead of gc_count += seq.nucparams.nuc_freq[nuc] 

imho have correct these wrong usages of class variables usage of object (instance) variables.