Split text to phrases and enumerate them

Question

I have this sequence:

>my_sequence
atccagcaaaaacgctccaaggattctcgactggactcattacttaatcagtattcgcaagcggacgccgaggtcgtaaaggctgaaaccgcacaatcggatgcgcccagtgatgacgcactxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxcgccttgcccacccaccgacaaccggtgagtgaaaaattggaacggtgattaaaxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxttgtgctttatttctggagggcggtgtttaggggtaggcgcgccatgttttttgccttcagcgatcccaggtacaaccagtccccatattcgcgcactgtcgtgatcggcgagtaattacctgtgctcgcatcttgcaggttggcaatcaccttgccgtccaagtccagacccagtgcaaaggcacgcttttccatgggtttgggcagtaccgtcaatgcccgaacaatcattttgc

I want to split this long sequence eliminating the "xxxxx" and create separated sequences like this:

>1
atccagcaaaaacgctccaaggattctcgactggactcattacttaatcagtattcgcaagcggacgccgaggtcgtaaaggctgaaaccgcacaatcggatgcgcccagtgatgacgcact
>2
cgccttgcccacccaccgacaaccggtgagtgaaaaattggaacggtgattaaa  
>3
ttgtgctttatttctggagggcggtgtttaggggtaggcgcgccatgttttttgccttcagcgatcccaggtacaaccagtccccatattcgcgcactgtcgtgatcggcgagtaattacctgtgctcgcatcttgcaggttggcaatcaccttgccgtccaagtccagacccagtgcaaaggcacgcttttccatgggtttgggcagtaccgtcaatgcccgaacaatcattttgc

Does anyone have any idea to start?

Thank you.

1st step: `biopython` for parser fasta file. It's a good way — Jose Ricardo Bustos M., Mar 21 '17 at 14:06
@JoseRicardoBustosM. How about putting all those steps in an answer? — Ma0, Mar 21 '17 at 14:13
@Ev.Kounis the question is `Does anyone have any idea to start?` .... It's not like finishing — Jose Ricardo Bustos M., Mar 21 '17 at 14:18

Rushy Panchal · Accepted Answer · 2017-03-21T14:10:00.677

A simple way would be to first split on each "x" character, and then filter out the empty results:

sequences = filter(None, my_sequence.split("x"))

Here, the None argument to filter means to only keep truthy-values – empty strings are treated as false, so they will be removed from the results.

Note: In Python 3, filter returns an iterator so if you want a list, use:

sequences = list(filter(None, my_sequence.split("x")))

For example:

In [5]: filter(str, my_sequence.split("x"))
Out[5]: 
['atccagcaaaaacgctccaaggattctcgactggactcattacttaatcagtattcgcaagcggacgccgaggtcgtaaaggctgaaaccgcacaatcggatgcgcccagtgatgacgcact',
 'cgccttgcccacccaccgacaaccggtgagtgaaaaattggaacggtgattaaa',
 'ttgtgctttatttctggagggcggtgtttaggggtaggcgcgccatgttttttgccttcagcgatcccaggtacaaccagtccccatattcgcgcactgtcgtgatcggcgagtaattacctgtgctcgcatcttgcaggttggcaatcaccttgccgtccaagtccagacccagtgcaaaggcacgcttttccatgggtttgggcagtaccgtcaatgcccgaacaatcattttgc']

Another solution is to use regular expressions. If you have a variable amount of "x" characters between the sequences, you can split on the x+ pattern, which matches one or more x's in a row.

For example:

In [6]: import re
In [7]: p = re.compile(r'x+')
In [8]: p.split(my_sequence)
Out[8]: 
['atccagcaaaaacgctccaaggattctcgactggactcattacttaatcagtattcgcaagcggacgccgaggtcgtaaaggctgaaaccgcacaatcggatgcgcccagtgatgacgcact',
 'cgccttgcccacccaccgacaaccggtgagtgaaaaattggaacggtgattaaa',
 'ttgtgctttatttctggagggcggtgtttaggggtaggcgcgccatgttttttgccttcagcgatcccaggtacaaccagtccccatattcgcgcactgtcgtgatcggcgagtaattacctgtgctcgcatcttgcaggttggcaatcaccttgccgtccaagtccagacccagtgcaaaggcacgcttttccatgggtttgggcagtaccgtcaatgcccgaacaatcattttgc']

can you cast that to `list` for Python 3 users? – Ma0 Mar 21 '17 at 14:05 — Ma0, Mar 21 '17 at 14:05

score 2 · Answer 2 · answered Mar 21 '17 at 14:09

If you want to have a single entry for each sequence of x-s you can use regular expressions:

import re
x = 'atccagcaaaaacgctccaaggattctcgactggactcattacttaatcagtattcgcaagcggacgccgaggtcgtaaaggctgaaaccgcacaatcggatgcgcccagtgatgacgcactxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxcgccttgcccacccaccgacaaccggtgagtgaaaaattggaacggtgattaaaxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxttgtgctttatttctggagggcggtgtttaggggtaggcgcgccatgttttttgccttcagcgatcccaggtacaaccagtccccatattcgcgcactgtcgtgatcggcgagtaattacctgtgctcgcatcttgcaggttggcaatcaccttgccgtccaagtcc
agacccagtgcaaaggcacgcttttccatgggtttgggcagtaccgtcaatgcccgaacaatcattttgc'
re.split(r'x+', x)
>['atccagcaaaaacgctccaaggattctcgactggactcattacttaatcagtattcgcaagcggacgccgaggtcgtaaaggctgaaaccgcacaatcggatgcgcccagtgatgacgcact',
 'cgccttgcccacccaccgacaaccggtgagtgaaaaattggaacggtgattaaa',
 'ttgtgctttatttctggagggcggtgtttaggggtaggcgcgccatgttttttgccttcagcgatcccaggtacaaccagtccccatattcgcgcactgtcgtgatcggcgagtaattacctgtgctcgcatcttgcaggttggcaatcaccttgccgtccaagtccagacccagtgcaaaggcacgcttttccatgggtttgggcagtaccgtcaatgcccgaacaatcattttgc']

Here r'x+' means I will split the original string on a sequence of one or more x-s.

Chiheb Nexus · Answer 3 · 2017-03-21T15:26:38.463

Another way to have the desired output is using list comprehension.

This is an example:

# Or maybe a generator
# data = (k for k in my_sequence.split("x") if k)
data = [k for k in my_sequence.split("x") if k]

for k,v in enumerate(data):
    print("{0} >>> {1}".format(k,v))

Output:

0 >>> atccagcaaaaacgctccaaggattctcgactggactcattacttaatcagtattcgcaagcggacgccgaggtcgtaaaggctgaaaccgcacaatcggatgcgcccagtgatgacgcact
1 >>> cgccttgcccacccaccgacaaccggtgagtgaaaaattggaacggtgattaaa
2 >>> ttgtgctttatttctggagggcggtgtttaggggtaggcgcgccatgttttttgccttcagcgatcccaggtacaaccagtccccatattcgcgcactgtcgtgatcggcgagtaattacctgtgctcgcatcttgcaggttggcaatcaccttgccgtccaagtccagacccagtgcaaaggcacgcttttccatgggtttgggcagtaccgtcaatgcccgaacaatcattttgc

Split text to phrases and enumerate them

3 Answers3