[Tutor] triple-nested for loop not working

[bob gailer]

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