R：如何在序列比对开始时计算缺口？

Question

I am analyzing an alignment of amino acid sequences using R and need a reproducible way to figure out where the start is for each sequence. My alignment can be read in as a data frame. Here is a sample of 3.

alignment <- data.frame("Strains" = c("Strain.1", "Strain.2", "Strain.3"),
               "Sequence" = c("MASLIYRQLLTNSYTVNLSDEIQNIGSAKSQDVTINPGPFAQTGYAPVNWGAGETNDSTTVEPLLDGPYQPTTFNPPTSYWILLAPTAEGVVIQGTNNTDRWLATILIEPNVQATNRTYNLFGQQETLLVENTSQTQWKFVDVSKTTSTGSYTQHGPLFSTPKLYAVMKFSGKIYTYNGTTPNAA-TGY-YSTTSYDTVNMTSSCDFYIIPRSQEGKCTEYINYGLPPIQNTRNVVPVALSAREIVHTRAQVNEDIVVSKTSLWKEMQYNRDITIRFKFDRTIIKAGGLGYKWSEISFKPITYQYTYTRDGEQITAHTTCSVNGVNNFSYNGGSL---------------------",
                 "MASLIYRQLLTNSYTVNLSDEIQNIGSAKSQDVTINPGPFAQTGYAPVNWGAGETNDSTTVEPLLDGPYQPTTFNPPTSYWILLAPTAEGVVIQGTNNTDRWLATILIEPNVQATNRTYNLFGQQETLLVENTSQTQWKFVDVSKTTSTGSYTQHGPLFSTPKLYAVMKFSGKIYTYNGTTPNAA-TGY-YSTTSYDTVNMTSSCDFYIIPRSQEGKCTEYINYGLPPIQNTRNVVPVALSAREIVHTRAQVNEDIVVSKTSLWKEMQYNRDITIRFKFDRTIIKAGGLGYKWSEISFKPITYQYTYTRDGEQITAHTTCSVNGVNNFSYNGGSLPTDFAIS--------------",
                 "-----------------------NIGSAKSQDVTINPGPFAQTGYAPVNWGAGETNDSTTVEPLLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNVDRWLATILIEPNVQATNRTYNLFGQQEILLIENTSQTQWKFVDVSKTTPTGSYTQHGPLFSTPKLYAVMKFSGKIYTYNGTTPNVT-TGY-YSTTNYDTVNMT-----------------------------------------------------"))

Each of the dashes represents a space. What I want to do is read through my data frame and count how many spaces are at the beginning of each sequence. So far I've tried using the str_count function. For example:

alignment$shift <- str_count(alignment$Sequence, "-")

but this fails me when I have gaps downstream in my sequence. Really I'm only interested in the gaps that occur at the beginning of the sequences.

I stumbled across the regex function in a post that almost perfectly matches my problem, ( How to count the number of hyphens at the beginning of a string in javascript? ) but this is in Java and I'm not sure how to translate this to R.

My questions are:

1) Is it possible to have str_count stop looking for "-" characters once it reaches a non-"-" character?

2) Is there a way to use regex or a similar function in R that outputs the length of a character match at the beginning of a string?

Answer 1

You could do this...

alignment$Sequence <- as.character(alignment$Sequence) #in case they are factors (as above)

alignment$shift <- nchar(alignment$Sequence) - nchar(gsub("^-+", "", alignment$Sequence))

alignment$shift
[1]  0  0 23

It just counts the number of characters removed by telling gsub to delete the start of a string (the ^ ) followed by any number of spaces ( -+ ). You could use str_replace instead of gsub .

Answer 2

Maybe this might help? It'll return the position index of the start and end of the "---" string only if it begins at the start of the string.

library(stringr)

str_locate_all(string = alignment$Sequence, pattern = "^-{1,}[A-Z]")
[[1]]
     start end

[[2]]
     start end

[[3]]
     start end
[1,]     1  24