Loops for sequence output - python

Question

I've been struggling to figure out a way to get my sequence printed out with a 6-mer in the sequence on separate lines. As so (note the spacing of each line):

atgctagtcatc
 tgctag
  gctagt
   ctagtc
    tagtca
     etc

So far, I've been able to get my sequence in string as shown:

from Bio import SeqIO
record = SeqIO.read(open("testSeq.fasta"), "fasta")
sequence = str(record.seq)

However, the only way I could seem to figure out to do the printing of the 6-mers is by:

print sequence 
print sequence[0:5]
print "", sequence[1:6]
print "", "", sequence[2:7]
print "", "", "", sequence [3:8]
etc

I feel like there should be an easier way to do this. I've tried this, but it doesn't seem to work:

x = 0
y = 6
for sequence in sequence[x:y]
    print sequence
    x = x + 1
    y = y + 1

Any opinions on how I should be attempting to accomplish this task would be greatly appreciated. I've only been using python for a couple days now and I'm sorry if my question seems simple.

Thank you!!

True, but any comma separation is replaced with a space when printed. — tmr232
– tmr232, Commented Feb 19, 2015 at 21:23

tmr232 · Accepted Answer · 2015-02-19 21:21:59Z

2

This should work:

width = 6
for i in range(len(sequence) - width):
    print " " * i + sequence[i:i+width]

answered Feb 19, 2015 at 21:21

tmr232

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ljetibo · Accepted Answer · 2015-02-19 21:22:36Z

0

You could try the following (as far as I see you're using python2)

seq = "atgctagtcatc"
spaces = " "
for i in range(0, len(seq)):
    print spaces*i+seq[i:i+6]

Output:

atgcta
 tgctag
  gctagt
   ctagtc
    tagtca
     agtcat
      gtcatc
       tcatc
        catc
         atc
          tc
           c

answered Feb 19, 2015 at 21:22

ljetibo

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