x = 'cd4'
j=0
legend_text=[]
for pt in pts:
        new_dir = CWD + '\\' + pt
        os.chdir(new_dir)

        #Import alpha and beta chain data
        fileA = 'TRA' + str(x) + '_productive_' + pt + '.txt'
        fileB = 'TRB' + str(x) + '_productive_' + pt + '.txt'
        TRA = pd.read_csv(fileA, sep = '\t')
        TRB = pd.read_csv(fileB, sep = '\t')

        #Get clone size and frequency
        total_TCR = len(TRA) + len(TRB)

        for y in [TRA,TRB]:
            CloneSizes = y['nSeqCDR3'].value_counts()
            freq = CloneSizes.value_counts() / total_TCR
            plt.plot(freq,colors2[j])
            legend_text.append(str(y)+ str(x) + '_' + str(pt))
            j += 1

        os.chdir(CWD)

#Make the graph look pretty
plt.xscale('log')
plt.yscale('log')
plt.xlabel('Clone Size (log)')
plt.ylabel('Frequency (log)')
plt.title(x)
plt.legend(legend_text, loc = 'center right')
plt.show()