[Tutor] triple-nested for loop not working

[Spyros Charonis]

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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