On 03/23/2014 07:28 AM, Mustafa Musameh wrote:
Hi;
I have a file that looks like this:
title 1
AAATTTGGGCCCATA...
TTAACAAGTTAAAT…
title 2
AAATTTAAACCCGGGG…
ATATATATA…
…
I wrote the following to count the As, Cs, Gs anTs for each title I wrote the
following
import sys
file = open('file.fna')
data=file.readlines()
for line in data:
line = line.rstrip()
if line.startswith('>') :
print line
if not line.startswith('>') :
seq = line.rstrip()
counters={}
for char in seq:
counters[char] = counters.get(char,0) + 1
Ks = counters.keys()
Ks.sort()
for k in Ks:
print sum(counters.itervalues())
I want to get the following out put:
title
234
title 1
3453
….
but what i get
title 1
60
60
60
60
…
it seems it do counting for each line and print it out.
Can you help me please
Thanks
(Your code does not work at all, as is. Probably you did not just copy paste a
ruuning program.)
You are not taking into account the fact that there is a predefinite and small
set of of bases, which are the keys of the 'counters' dict. This would simplify
your code: see line below with "***". Example (adapted to python 3, and to read
a string directly, instead of a file):
data = """\
title 1
AAATTTGGGCCCATA
TTAACAAGTTAAAT
title 2
AAATTTAAACCCGGGG
ATATATATA
"""
for line in data.split("\n"):
line = line.strip()
if line == "": # for last line, maybe others
continue
if line.startswith('>'):
print(line)
continue
counters = {"A":0, "C":0, "G":0, "T":0} # ***
for base in line:
counters[base] += 1
bases = ["A","C","G","T"] # ***
for base in bases:
print(counters[base], end=" ")
print()
==>
title 1
5 3 3 4
7 1 1 5
title 2
6 3 4 3
5 0 0 4
Is this what you want?
denis
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