In [1]:

    

import cPickle as pickle


    

In [9]:

    

with open('GPD1_seq.fasta', 'r') as f: 
    lines = f.readlines()
seq=''
for line in lines:
    if line.startswith('>'): 
        continue
    else:        
        seq=seq + line.rstrip()
print seq


    

    




ATGTCTGCTGCTGCTGATAGATTAAACTTAACTTCCGGCCACTTGAATGCTGGTAGAAAGAGAAGTTCCTCTTCTGTTTCTTTGAAGGCTGCCGAAAAGCCTTTCAAGGTTACTGTGATTGGATCTGGTAACTGGGGTACTACTATTGCCAAGGTGGTTGCCGAAAATTGTAAGGGATACCCAGAAGTTTTCGCTCCAATAGTACAAATGTGGGTGTTCGAAGAAGAGATCAATGGTGAAAAATTGACTGAAATCATAAATACTAGACATCAAAACGTGAAATACTTGCCTGGCATCACTCTACCCGACAATTTGGTTGCTAATCCAGACTTGATTGATTCAGTCAAGGATGTCGACATCATCGTTTTCAACATTCCACATCAATTTTTGCCCCGTATCTGTAGCCAATTGAAAGGTCATGTTGATTCACACGTCAGAGCTATCTCCTGTCTAAAGGGTTTTGAAGTTGGTGCTAAAGGTGTCCAATTGCTATCCTCTTACATCACTGAGGAACTAGGTATTCAATGTGGTGCTCTATCTGGTGCTAACATTGCCACCGAAGTCGCTCAAGAACACTGGTCTGAAACAACAGTTGCTTACCACATTCCAAAGGATTTCAGAGGCGAGGGCAAGGACGTCGACCATAAGGTTCTAAAGGCCTTGTTCCACAGACCTTACTTCCACGTTAGTGTCATCGAAGATGTTGCTGGTATCTCCATCTGTGGTGCTTTGAAGAACGTTGTTGCCTTAGGTTGTGGTTTCGTCGAAGGTCTAGGCTGGGGTAACAACGCTTCTGCTGCCATCCAAAGAGTCGGTTTGGGTGAGATCATCAGATTCGGTCAAATGTTTTTCCCAGAATCTAGAGAAGAAACATACTACCAAGAGTCTGCTGGTGTTGCTGATTTGATCACCACCTGCGCTGGTGGTAGAAACGTCAAGGTTGCTAGGCTAATGGCTACTTCTGGTAAGGACGCCTGGGAATGTGAAAAGGAGTTGTTGAATGGCCAATCCGCTCAAGGTTTAATTACCTGCAAAGAAGTTCACGAATGGTTGGAAACATGTGGCTCTGTCGAAGACTTCCCATTATTTGAAGCCGTATACCAAATCGTTTACAACAACTACCCAATGAAGAACCTGCCGGACATGATTGAAGAATTAGATCTACATGAAGATTAG

In [14]:

    

def compute_nt_composition( sequence ):
    base_dict = {'A':0,'C':0,'G':0,'T':0}
    for elem in sequence:
        base_dict[elem]+=1
    return base_dict


    

In [20]:

    

result = compute_nt_composition(seq)
print result


    

    




{'A': 324, 'C': 240, 'T': 336, 'G': 276}

In [18]:

    

with open('save.p', 'w') as f:
    pickle.dump(result, f)


    

In [22]:

    

%matplotlib inline 
from pylab import *


    

In [35]:

    

xv=[0.7,1.7,2.7,3.7]; yv=[324,240,336,276]
mybar=bar(xv,yv,width=0.7)
xticks(range(1,5),['A','B','C','D'])
setp(mybar,color='g',edgecolor='k')


    

    
Out[35]:





[None, None, None, None, None, None, None, None]






    

In [ ]: