如何从R中的模糊字符串匹配返回实际匹配

Question

I have a load of DNA sequences and I need to be able to match the ones that have a certain string. However there is some variation in the target so Im matching with fuzzy matching. Id like to get the actual match rather than the whole sequence. agrep doesnt do this. Does anyone know of any package that does?

example dataframe RepeatAlusSequencesdf :

>chr1:61695-62229      aattccaagagtattattgcaccaaaaggcatggacttaaaattcttgatacatgatttcaaaatattttctttaaggtttgaatcagtctatattccctccagcagcgtataaaagtgccaatttctctgatccttagccagtttgggtaataataattgtaaaacttttttttctttttttttgagacagagtctccctctgtcgccaggctgaagtgcagtggcgcaatctcggctcactgcaacctccgcctcccggggtcaagctattctcctgcctcagcctcccaagtagctgggactacaggcatgcaccaccatgcccagctaatttttgttatttttagtagagatggagtttccccatgttggacaggatggtctcgatctcttgacctcgtgatccaccctcctcggcctcccaaagtgctgggataacaggcgtgaacaaccatgcccggcctgtaaaactttttcctaatttaacagaaaaataatagtattatattttatcatatttctttgatttcta

>chr1:101718-102194   taaaaataaatgtattaagtatgaacaacaaaaaagctagtaaaggttgaacaacaactatccttaggaaagtggaaataatgtattaataaatatgaaagcaggctagccacggtgactcacatctgtaatcccagcactttgggaggctgaggcaggcagatcacctgaggtcaggagttccagaccagcctggccaacatggtgaaatcttgtctctcctacaaatacaaaaactagccaggcttggttgtgcactcctgtaattcgagctacttgggaggctgaggcaggagaatctcttgaacctgagaggcagaggttgcagtgagccaagatcatgccactgcactccagctggggcaacagagtgacactccatctcaaaataaataaataagaaagcagaaactaataaactagaaaacagaaacatagaactaatttataaatcaaagcactatgccttgaaaaga

the code i used:

RepeatAlusSequencesdfMatch <- RepeatAlusSequencesdf[agrep("aacctcaaagactggcctca", RepeatAlusSequencesdf[,2],ignore.case = TRUE, max.distance = 0.3), ]

what Id like returned:

aacctcaaagactggcctca
aacctcattgactggcctca

rather than the whole sequence

Answer 1

There might be a specialized package to do this, but this works: I create a vector of substrings of the same length as the string you are looking to match. I then use agrep to identify the matched substrings.

#long string
s1<-"aattccaagagtattattgcaccaaaaggcatggacttaaaattcttgatacatgatttcaaaatattttctttaaggtttgaatcagtctatattccctccagcagcgtataaaagtgccaatttctctgatccttagccagtttgggtaataataattgtaaaacttttttttctttttttttgagacagagtctccctctgtcgccaggctgaagtgcagtggcgcaatctcggctcactgcaacctccgcctcccggggtcaagctattctcctgcctcagcctcccaagtagctgggactacaggcatgcaccaccatgcccagctaatttttgttatttttagtagagatggagtttccccatgttggacaggatggtctcgatctcttgacctcgtgatccaccctcctcggcctcccaaagtgctgggataacaggcgtgaacaaccatgcccggcctgtaaaactttttcctaatttaacagaaaaataatagtattatattttatcatatttctttgatttcta"
my.string <-"aacctcaaagactggcctca"
substrings <-substring(s1,seq(1,nchar(s1)-nchar(my.string)+1,1),seq(nchar(my.string),nchar(s1),1))
agrep(my.string, substrings,ignore.case = TRUE, max.distance = 0.35,value = TRUE)

[1] "caccaaaaggcatggactta" "accaaaaggcatggacttaa"