On Thu, Jan 28, 2010 at 4:31 PM, Krister Svanlund
<krister.svanl...@gmail.com> wrote:
> On Thu, Jan 28, 2010 at 4:28 PM, Krister Svanlund
> <krister.svanl...@gmail.com> wrote:
>> On Thu, Jan 28, 2010 at 4:07 PM, evilweasel
>> <karthikramaswam...@gmail.com> wrote:
>>> Hi folks,
>>>
>>> I am a newbie to python, and I would be grateful if someone could
>>> point out the mistake in my program. Basically, I have a huge text
>>> file similar to the format below:
>>>
>>> AAAAAGACTCGAGTGCGCGGA 0
>>> AAAAAGATAAGCTAATTAAGCTACTGG 0
>>> AAAAAGATAAGCTAATTAAGCTACTGGGTT 1
>>> AAAAAGGGGGCTCACAGGGGAGGGGTAT 1
>>> AAAAAGGTCGCCTGACGGCTGC 0
>>>
>>> The text is nothing but DNA sequences, and there is a number next to
>>> it. What I will have to do is, ignore those lines that have 0 in it,
>>> and print all other lines (excluding the number) in a new text file
>>> (in a particular format called as FASTA format). This is the program I
>>> wrote for that:
>>>
>>> seq1 = []
>>> list1 = []
>>> lister = []
>>> listers = []
>>> listers1 = []
>>> a = []
>>> d = []
>>> i = 0
>>> j = 0
>>> num = 0
>>>
>>> file1 = open(sys.argv[1], 'r')
>>> for line in file1:
>>> if not line.startswith('\n'):
>>> seq1 = line.split()
>>> if len(seq1) == 0:
>>> continue
>>>
>>> a = seq1[0]
>>> list1.append(a)
>>>
>>> d = seq1[1]
>>> lister.append(d)
>>>
>>>
>>> b = len(lister)
>>> for j in range(0, b):
>>> if lister[j] == 0:
>>> listers.append(j)
>>> else:
>>> listers1.append(j)
>>>
>>>
>>> print listers1
>>> resultsfile = open("sequences1.txt", 'w')
>>> for i in listers1:
>>> resultsfile.write('\n>seq' + str(i) + '\n' + list1[i] + '\n')
>>>
>>> But this isn't working. I am not able to find the bug in this. I would
>>> be thankful if someone could point it out. Thanks in advance!
>>>
>>> Cheers!
I'm trying this again:
newlines = []
with open(sys.argv[1], 'r') as f:
text = f.read();
for line in (l.strip() for l in text.splitlines()):
if line:
line_elem = line.split()
if len(line_elem) == 2 and line_elem[1] == '1':
newlines.append('seq'+line_elem[0])
with open(sys.argv[2], 'w') as f:
f.write('\n'.join(newlines))
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