On 5/4/2011 2:31 PM, Spyros Charonis wrote:
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 = []
Following line will fail, as finalmotifs is not defined. It appears to
be defined 10 lines later.
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:
Next 2 for statements both use i as the loop index. Even though the
program will run it is not a good idea.
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()
You need 2 loops, not 3. That is way overkill.You accomplish the same
thing with:
# open the 3 files
finalmotifs = motif_file.readlines()
for line in seqalign:
for item in finalmotifs:
if item in line:
align_file.write('~' * len(line) + '\n')
# close the 3 files
--
Bob Gailer
919-636-4239
Chapel Hill NC
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