Your problem is most likely here.
for line in seqalign:
for i in len(finalmotif_seqs): # for item in finalmotif_seqs:
for i in len(finalmotif_annot): # for item in finalmotif_annot:
instead of
for line in seqalign:
for i in xrange(len(finalmotif_seqs)): # for item in finalmotif_seqs:
for i in xrange(len(finalmotif_annot)): # for item in
finalmotif_annot:
len just returns one number. So for each loop, you are running through the loop
only once where i= whatever len returned.
>>> for x in (5,6,7,8):
... print x
...
5
6
7
8
Honestly, I am not sure why you are not getting the following error
>>> for x in len((5,6,7,8)):
... print x
...
TypeError: 'int' object is not iterable
I would also avoid using "i" as your nested loop counter. It might work in this
instance, but gives you more confusion and less flexibility. See the following
example
>>> for x in xrange(3):
... print "level 1=", x
... for x in xrange(4,5):
... print "level 2=", x
... for x in xrange(6,9):
... print "level 3=", x
...
level 1= 0
level 2= 4
level 3= 6
level 3= 7
level 3= 8
level 1= 1
level 2= 4
level 3= 6
level 3= 7
level 3= 8
level 1= 2
level 2= 4
level 3= 6
level 3= 7
level 3= 8
Instead use separate variables. This allows for easier understandability and
for accessing them from nested loop levels.
>>> for x in xrange(3):
... print "level 1=", x
... for y in xrange(4,5):
... print "level 2=", y
... for z in xrange(6,9):
... print "level 3=", z, ' | level 2=', y , ' | level 1=', x
...
level 1= 0
level 2= 4
level 3= 6 | level 2= 4 | level 1= 0
level 3= 7 | level 2= 4 | level 1= 0
level 3= 8 | level 2= 4 | level 1= 0
level 1= 1
level 2= 4
level 3= 6 | level 2= 4 | level 1= 1
level 3= 7 | level 2= 4 | level 1= 1
level 3= 8 | level 2= 4 | level 1= 1
level 1= 2
level 2= 4
level 3= 6 | level 2= 4 | level 1= 2
level 3= 7 | level 2= 4 | level 1= 2
level 3= 8 | level 2= 4 | level 1= 2
Ramit
Ramit Prasad | JPMorgan Chase Investment Bank | Currencies Technology
712 Main Street | Houston, TX 77002
work phone: 713 - 216 - 5423
From: tutor-bounces+ramit.prasad=jpmchase....@python.org
[mailto:tutor-bounces+ramit.prasad=jpmchase....@python.org] On Behalf Of Spyros
Charonis
Sent: Wednesday, May 04, 2011 1:31 PM
To: tutor
Subject: [Tutor] triple-nested for loop not working
Hello everyone,
I have written a program, as part of a bioinformatics project, that extracts
motif sequences (programmatically just strings of letters) from a database and
writes them to a file.
I have written another script to annotate the database file (in plaintext ASCII
format) by replacing every match of a motif with a sequence of tildes (~).
Primitive I know, but not much more can be done with ASCII files. The code
goes as follows:
motif_file = open('myfolder/pythonfiles/final motifs_11SGLOBULIN', 'r') # =>
final motifs_11sglobulin contains the output of my first program
align_file = open('myfolder/pythonfiles/11sglobulin.seqs', 'a+') # =>
11sglobulin.seqs is the ASCII sequence alignment file which I want to
"annotate" (modify)
finalmotif_seqs = []
finalmotif_length = [] # store length of each motif
finalmotif_annot = []
for line in finalmotifs:
finalmotif_seqs.append(line)
mot_length = len(line)
finalmotif_length.append(mot_length)
for item in finalmotif_length:
annotation = '~' * item
finalmotif_annot.append(annotation)
finalmotifs = motif_file.readlines()
seqalign = align_file.readlines()
for line in seqalign:
for i in len(finalmotif_seqs): # for item in finalmotif_seqs:
for i in len(finalmotif_annot): # for item in finalmotif_annot:
if finalmotif_seqs[i] in line: # if item in line:
newline = line.replace(finalmotif_seqs[i], finalmotif_annot[i])
#sys.stdout.write(newline) # => print the lines out on
the shell
align_file.writelines(newline)
motif_file.close()
align_file.close()
My coding issue is that although the script runs, there is a logic error
somewhere in the triple-nested for loop as I when I check my file I'm
supposedly modifying there is no change. All three lists are built correctly
(I've confirmed this on the Python shell). Any help would be much appreciated!
I am running Python 2.6.5
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