Unable to extract postfixes using regular expression in R

user_19802062 0
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I am working on Single Cell RNA, and trying to demultiplex RAW count matrix. I am following this. In this tutorial, the barcode is in this format: "BIOKEY_33_Pre_AAACCTGAGAGACTTA-1". Where BIOKEY13_Pre is the prefix and AAACCTGCAACAACCT-1 is the sequence of bases. The prefixes are sample names, so they will be used to demultiplex the data.

Using this regular expression, I can extract the prefixes. data.pfx <- gsub("(.+)_[A-Z]+-1$", "\\1", colnames(data.count), perl=TRUE).

The problem is, in my data, the barcode is in this format: AAACCTGAGAAACCGC_LN_05 where the sequence is first, and the sample name is last. I need to extract postfixes. If I run the above regular expression on my data, I get the following output:

data.pfx <- gsub("(.+)_[A-Z]+-1$", "\\1", colnames(data.count), perl=TRUE)
sample.names <- unique(data.pfx)
head(sample.names)
"AAACCTGAGAAACCGC_LN_05" 
"AAACCTGAGAAACGCC_NS_13"
"AAACCTGAGCAATATG_LUNG_N34"

The desired output:
"LN_05"
"NS_13"
"LUNG_N34"
r regex
2 Answers

You can use

sub(".*_([A-Z]+_[0-9A-Z]+)$", "\\1", sample.names)

See the regex demo.

Details:

  • .* - any zero or more chars as many as possible
  • _ - an underscore
  • ([A-Z]+_[0-9A-Z]+) - Group 1 (\1): one or more uppercase ASCII letters, _ and one or more uppercase ASCII letters o digits
  • $ - end of string.
user_38329700

A bit easier by just removing all leading capital letters up to and including the first underscore

sample.names <- c("AAACCTGAGAAACCGC_LN_05" ,
                  "AAACCTGAGAAACGCC_NS_13")
sub("^[A-Z]+_", "", sample.names)
#> [1] "LN_05" "NS_13"
user_81073620
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