hashing a sequence

[kdt]

Hi
i have a sequence of characters that I need to perform analysis on. I want to be able to generate a table with unique substrings of length n and their positions. A hash table was used in perl, not sure of the python equivelent .

sequence = 'gtccaaagtt'

trying to get the output into a table with substring in one column and position(s). for the above sequence this could be something like;
aa 4,5

i have the following code:

def split_len(seq, length):
      return [seq[i:i+length] for i in range(0, len(seq), length)]

but it doesnt store locations or take into consideration repeats.

been searching google for two days now Sad please help
thanks

[ghostdog74]

Hi
i have a sequence of characters that I need to perform analysis on. I want to be able to generate a table with unique substrings of length n and their positions. A hash table was used in perl, not sure of the python equivelent .

sequence = 'gtccaaagtt'

trying to get the output into a table with substring in one column and position(s). for the above sequence this could be something like;
aa 4,5

i have the following code:

def split_len(seq, length):
      return [seq[i:i+length] for i in range(0, len(seq), length)]

but it doesnt store locations or take into consideration repeats.

been searching google for two days now Sad please help
thanks

dictionaries are the equivalent of hashes in Perl. your piece of code actually splits the seq according to length given
eg

>>> length=3
>>> [seq[i:i+length] for i in range(0, len(seq), length)]
['gtc', 'caa', 'agt', 't']
 

can you describe the output you want again?

[kdt]

dictionaries are the equivalent of hashes in Perl. your piece of code actually splits the seq according to length given
eg

>>> length=3
>>> [seq[i:i+length] for i in range(0, len(seq), length)]
['gtc', 'caa', 'agt', 't']
 

can you describe the output you want again?

thanks for the quick reply. i was wanting the sequence to be split, but i think im going about it the wrong way. i want to take a sequence, break it up substrings of length n and record the position occurrence of the substrings in the query string. So for example for the sequence "attgccatgc", specifying n=2 i would like a dictionary with:
string position
at 1,7
tt 2
tg 3,8
gc 4,9
etc...

hope this helps

thanks

[bvdet]

thanks for the quick reply. i was wanting the sequence to be split, but i think im going about it the wrong way. i want to take a sequence, break it up substrings of length n and record the position occurrence of the substrings in the query string. So for example for the sequence "attgccatgc", specifying n=2 i would like a dictionary with:
string position
at 1,7
tt 2
tg 3,8
gc 4,9
etc...

hope this helps

thanks

Like this?

import re
 
def indexList(s, item, i=0):
    i_list = []
    while True:
        try:
            i = s.index(item, i)
            i_list.append(i)
            i += 1
        except:
            break
    return i_list
 
s = 'Having the base plate subassembly mark at each column will do two things - reference the large scale base plate details and provide the checker with a check of the column bases in the model without having to check each column in the model.'
 
sub_length = 4
 
subList = [s[i:i+sub_length] for i in range(len(s)) if re.match(r'[a-z]{%s}' % sub_length, s[i:i+sub_length])]
 
dd = {}
for subi in subList:
    if not dd.has_key(subi):
        dd[subi] = indexList(s, subi)
 
for key in dd:
    print '%s = %s' % (key, dd[key])

>>> ence = [80]
renc = [79]
fere = [77]
scal = [95]
thin = [66]
colu = [47, 164, 219]
ving = [2, 200]
mode = [184, 233]
ovid = [126]
..........................

[kdt]

thanks btdev, works a treat :)