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In R or Python, How do I implement an allele sequence "autocomplete" tool given a dictionary of possible allele sequence matches?

In R or Python, how do I implement an allele sequence "autocomplete" tool given a dictionary of possible allele sequence matches?

That is, given, say an allele sequence: 

CC_ATCGATCGTA_GATCGGCAA_GTGA

And given a limited number of dictionary values:

Allele 1: CCGATCGATCGTACGATCGGCAAGGTGA
Allele 2: ACTATCTATCGTAAGATCGGCAACGTGG
Allele 3: CCAATCGATCGTACGATCGGCAACGTGA
Allele 4: TCTATCTATCGTAAGATCGGCAACGTGG

The program will return to me Allele 1 and Allele 3 as possible reconstructions of the original allele sequence. Since:

Original: 

CC_ATCGATCGTA_GATCGGCAA_GTGA

Matches: 

Allele 1: CCGATCGATCGTACGATCGGCAAGGTGA
Allele 3: CCAATCGATCGTACGATCGGCAACGTGA

Ideally, the tool will search through the dictionary values as a tree search rather than exhaustively comparing the incomplete string with each dictionary entry. In other words, upon comparison of the first letter of alleles 2 and 3, they are automatically eliminated from consideration given that the first nucleotide does not match with the original string.

snp sequencing r python assembly
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updated by zx8754 zx8754 • written by kristopherfernandez • kristopherfernandez

I would zip() the strings and iterate over the pairs, break if mismatch, continue if _ and return if reached the end

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written by WouterDeCoster WouterDeCoster

2 answers

There's a lot of ways to do it, depending how large your dictionary is, or how often/quickly those are queried.

My intuition is that you probably want to use a Trie structure where you would insert all your alleles, and then query your trie once it's built.

I wrote a quick solution using LexPy:

from lexpy.trie import Trie
trie = Trie()
input_alleles = [
    "CCGATCGATCGTACGATCGGCAAGGTGA",
    "ACTATCTATCGTAAGATCGGCAACGTGG",
    "CCAATCGATCGTACGATCGGCAACGTGA",
    "TCTATCTATCGTAAGATCGGCAACGTGG"
]

trie.add_all(input_alleles)

query = "CC_ATCGATCGTA_GATCGGCAA_GTGA"
query_dist = query.count("_")

matches = trie.search_within_distance(query, dist=query_dist)

print matches

Results:

python trie-demo.py
['CCAATCGATCGTACGATCGGCAACGTGA', 'CCGATCGATCGTACGATCGGCAAGGTGA']

Further readings:

https://en.wikipedia.org/wiki/Trie
https://en.wikipedia.org/wiki/Finite-state_machine
https://en.wikipedia.org/wiki/Suffix_tree

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written by mbelmadani mbelmadani

Amazing! I am new to computer programming and learning these things really help me add new skills to my toolbox. So for that, thank you!

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written by kristopherfernandez • kristopherfernandez

There must be some ready R packages for this specific task, but here is a simple one using agrep (not sure how well this will perform, but works for your example input):

x <- "CC_ATCGATCGTA_GATCGGCAA_GTGA"

y <- c("CCGATCGATCGTACGATCGGCAAGGTGA",
       "ACTATCTATCGTAAGATCGGCAACGTGG",
       "CCAATCGATCGTACGATCGGCAACGTGA",
       "TCTATCTATCGTAAGATCGGCAACGTGG")

y[ agrep(x, y) ]
# [1] "CCGATCGATCGTACGATCGGCAAGGTGA" "CCAATCGATCGTACGATCGGCAACGTGA"
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written by zx8754 zx8754

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