[Tutor] triple-nested for loop not working

[Alan Gauld]

"Spyros Charonis" <s.charonis at gmail.com> wrote

> motif_file = open('myfolder/pythonfiles/final motifs_11SGLOBULIN', 
> 'r')
> align_file = open('myfolder/pythonfiles/11sglobulin.seqs', 'a+')

> finalmotif_seqs = []
> finalmotif_length = []  # store length of each motif
> finalmotif_annot = []
>
> finalmotifs = motif_file.readlines()
> seqalign = align_file.readlines()

NB. I've moved the lines to after the initialisation, but...

> 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)

This seems very verbose. Why not go directly to the tildes?

for line in finalmotifs:
     finalmotof_seqs.append(line)
     finalmotif_annot.append('~' * len(line))

You don't seem to use the list of lens for anything else?

> for line in seqalign:
>    for i in len(finalmotif_seqs):      # for item in 
> finalmotif_seqs:

len() returns an integer not a sequence so you can't
iterate over it, you would need range(), but...

>        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)

You comments are better python than your code is!

with  open(align_file) as seqalign:
        for line in seqalign:
             for seq in finalmotif_seqs:
                  for annot in finalmotif_annot:
                      line = line.replace(seq, annot)  # +'\n'???
                      align_file.write(line)

> motif_file.close()
> align_file.close()

If you use 'with' you don't need these...

HTH,

-- 
Alan Gauld
Author of the Learn to Program web site
http://www.alan-g.me.uk/