Tuesday 10 March 2015

Program in python to find the total number of lines in file containing nucleotide sequence in FASTA format

First of all what you need to do is save a FASTA format of any gene in a text file.

fr = open('C:\\Users\\Administrator\\Desktop\\interleukin.txt','r')
print(fr)
fr.close()
fr = open('C:\\Users\\Administrator\\Desktop\\interleukin.txt')
a1= fr.read()  
line=a1.split('\n') # split the \n to divide sequence into indexes and remove the  description part of fasta format leaving only nucleotide sequence
lines=line[1:-2]   #start from 1st index terminating 0 index
print(lines)
print("total lines in the sequence is", len(lines))
print("length of last line is", len(lines[-1]))
fr.close()
print('first seven: ', len(a))   
a = fr.read(7)   # to get the first seven characters
print(a)



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