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 not totaly sure what you want to do but try this (python2.6+):
newlines = []
with open(sys.argv[1], 'r') as f:
text = f.read();
for line in text.splitlines():
if not line.strip() and line.strip().endswith('1'):
newlines.append('seq'+line)
with open(sys.argv[2], 'w') as f:
f.write('\n'.join(newlines))
--
http://mail.python.org/mailman/listinfo/python-list
