I have a vector of names where some names have leading and trailing . characters, and some do not. Here is an example:
test <- c('.name.1.','name.2','.name.3.')
I would like to conditionally remove leading and trailing . characters in these names, to return
c('name.1','name.2','name.3')
Use regular expressions:
test <- c('.name.1.','name.2','.name.3.')
gsub('^\\.|\\.$', '', test)
# [1] "name.1" "name.2" "name.3"
The two backslashes, \\, in the regular expression escape the dot, ., which would actually mean any character. The caret, ^, marks the beginning of the string, the dollar, $, the end of the string. The pipe, |, is a logical "or". So in essence the regular expression matches a dot at the beginning of the string or a dot at the end of the string and replaces it with an empty string.
More information on regular expressions can be found here and information on gsub and related functions here.
A quick function using the substr function:
fun1 <- function(x) substr(x, 1 + (1 * as.numeric(substr(x,1,1)=='.')), nchar(x) - (1 * as.numeric(substr(x, nchar(x), nchar(x)) == '.')))
We use substr to check for a . in the first and last elements of the string, then we use substr again to extract certain parts of the text. For example, if there is a . in the first character, but not in the second, we'll extract: substr(text, 2, nchar(text)).
fun1(test)
[1] "name.1" "name.2" "name.3"
Just for fun, here is a method with substring and grepl.
substring(test, 1L + grepl("^\\.", test), nchar(test) - grepl("\\.$", test))
[1] "name.1" "name.2" "name.3"
This will work replacing substring with substr. The cool thing about these functions is that they take vectors for their second and third arguments. Here, we can use grepl to increment between 1L and 2L for the second argument and between the position of the final character and the penultimate character.
You can also use str_extract from stringr:
library(stringr)
str_extract(test, "\\w+\\.\\d")
or str_replace_all (stringr-equivalent to gsub):
str_replace_all(test, "[.](.+)[.]", "\\1")
# [1] "name.1" "name.2" "name.3"
Related
I have the string in R
BLCU142-09|Apodemia_mejicanus
and I would like to get the result
Apodemia_mejicanus
Using the stringr R package, I have tried
str_replace_all("BLCU142-09|Apodemia_mejicanus", "[[A-Z0-9|-]]", "")
# [1] "podemia_mejicanus"
which is almost what I need, except that the A is missing.
You can use
sub(".*\\|", "", x)
This will remove all text up to and including the last pipe char. See the regex demo. Details:
.* - any zero or more chars as many as possible
\| - a | char (| is a special regex metacharacter that is an alternation operator, so it must be escaped, and since string literals in R can contain string escape sequences, the | is escaped with a double backslash).
See the R demo online:
x <- c("BLCU142-09|Apodemia_mejicanus", "a|b|c|BLCU142-09|Apodemia_mejicanus")
sub(".*\\|", "", x)
## => [1] "Apodemia_mejicanus" "Apodemia_mejicanus"
We can match one or more characters that are not a | ([^|]+) from the start (^) of the string followed by | in str_remove to remove that substring
library(stringr)
str_remove(str1, "^[^|]+\\|")
#[1] "Apodemia_mejicanus"
If we use [A-Z] also to match it will match the upper case letter and replace with blank ("") as in the OP's str_replace_all
data
str1 <- "BLCU142-09|Apodemia_mejicanus"
You can always choose to _extract rather than _remove:
s <- "BLCU142-09|Apodemia_mejicanus"
stringr::str_extract(s,"[[:alpha:]_]+$")
## [1] "Apodemia_mejicanus"
Depending on how permissive you want to be, you could also use [[:alpha:]]+_[[:alpha:]]+ as your target.
I would keep it simple:
substring(my_string, regexpr("|", my_string, fixed = TRUE) + 1L)
Is it possible to parse a vector of character strings to an alternation element in a regular expression? For example:
pattern <- "^This\\s(*alternation element*)\\srocks\\."
Animals <- c("cow","dog","cat")
So if I would then parse "Animals" to the regular expression it would result in:
pattern <- "^This\\s(*cow|dog|cat*)\\srocks\\."
It should basically work like or1() from the rebus package.
You could use paste0 to generate your regex :
paste0('^This\\s(', paste0(Animals, collapse = "|"), ')\\ssrocks\\.')
#[1] "^This\\s(cow|dog|cat)\\ssrocks\\."
Note than in R, you need to use double backslash (\\).
We can use sprintf
sprintf("^Thi\\s(%s)\\ssrocks\\.", paste(Animals, collapse="|"))
#[1] "^Thi\\s(cow|dog|cat)\\ssrocks\\."
Col
WBU-ARGU*06:03:04
WBU-ARDU*08:01:01
WBU-ARFU*11:03:05
WBU-ARFU*03:456
I have a column which has 75 rows of variables such as the col above. I am not quite sure how to use gsub or sub in order to get up until the integers after the first colon.
Expected output:
Col
WBU-ARGU*06:03
WBU-ARDU*08:01
WBU-ARFU*11:03
WBU-ARFU*03:456
I tried this but it doesn't seem to work:
gsub("*..:","", df$col)
Following may help you here too.
sub("([^:]*):([^:]*).*","\\1:\\2",df$dat)
Output will be as follows.
> sub("([^:]*):([^:]*).*","\\1:\\2",df$dat)
[1] "WBU-ARGU*06:03" "WBU-ARDU*08:01" "WBU-ARFU*11:03" "WBU-ARFU*03:456b"
Where Input for data frame is as follows.
dat <- c("WBU-ARGU*06:03:04","WBU-ARDU*08:01:01","WBU-ARFU*11:03:05","WBU-ARFU*03:456b")
df <- data.frame(dat)
Explanation: Following is only for explanation purposes.
sub(" ##using sub for global subtitution function of R here.
([^:]*) ##By mentioning () we are keeping the matched values from vector's element into 1st place of memory(which we could use later), which is till next colon comes it will match everything.
: ##Mentioning letter colon(:) here.
([^:]*) ##By mentioning () making 2nd place in memory for matched values in vector's values which is till next colon comes it will match everything.
.*" ##Mentioning .* to match everything else now after 2nd colon comes in value.
,"\\1:\\2" ##Now mentioning the values of memory holds with whom we want to substitute the element values \\1 means 1st memory place \\2 is second memory place's value.
,df$dat) ##Mentioning df$dat dataframe's dat value.
You may use
df$col <- sub("(\\d:\\d+):\\d+$", "\\1", df$col)
See the regex demo
Details
(\\d:\\d+) - Capturing group 1 (its value will be accessible via \1 in the replacement pattern): a digit, a colon and 1+ digits.
: - a colon
\\d+ - 1+ digits
$ - end of string.
R Demo:
col <- c("WBU-ARGU*06:03:04","WBU-ARDU*08:01:01","WBU-ARFU*11:03:05","WBU-ARFU*03:456")
sub("(\\d:\\d+):\\d+$", "\\1", col)
## => [1] "WBU-ARGU*06:03" "WBU-ARDU*08:01" "WBU-ARFU*11:03" "WBU-ARFU*03:456"
Alternative approach:
df$col <- sub("^(.*?:\\d+).*", "\\1", df$col)
See the regex demo
Here,
^ - start of string
(.*?:\\d+) - Group 1: any 0+ chars, as few as possible (due to the lazy *? quantifier), then : and 1+ digits
.* - the rest of the string.
However, it should be used with the PCRE regex engine, pass perl=TRUE:
col <- c("WBU-ARGU*06:03:04","WBU-ARDU*08:01:01","WBU-ARFU*11:03:05","WBU-ARFU*03:456")
sub("^(.*?:\\d+).*", "\\1", col, perl=TRUE)
## => [1] "WBU-ARGU*06:03" "WBU-ARDU*08:01" "WBU-ARFU*11:03" "WBU-ARFU*03:456"
See the R online demo.
sub("(\\d+:\\d+):\\d+$", "\\1", df$Col)
[1] "WBU-ARGU*06:03" "WBU-ARDU*08:01" "WBU-ARFU*11:03" "WBU-ARFU*03:456"
Alternatively match what you want (instead of subbing out what you don't want) with stringi:
stringi::stri_extract_first(df$Col, regex = "[A-Z-\\*]+\\d+:\\d+")
Slightly more concise stringr:
stringr::str_extract(df$Col, "[A-Z-\\*]+\\d+:\\d+")
# or
stringr::str_extract(df$Col, "[\\w-*]+\\d+:\\d+")
Suppose I have the following two strings and want to use grep to see which match:
business_metric_one
business_metric_one_dk
business_metric_one_none
business_metric_two
business_metric_two_dk
business_metric_two_none
And so on for various other metrics. I want to only match the first one of each group (business_metric_one and business_metric_two and so on). They are not in an ordered list so I can't index and have to use grep. At first I thought to do:
.*metric.*[^_dk|^_none]$
But this doesn't seem to work. Any ideas?
You need to use a PCRE pattern to filter the character vector:
x <- c("business_metric_one","business_metric_one_dk","business_metric_one_none","business_metric_two","business_metric_two_dk","business_metric_two_none")
grep("metric(?!.*_(?:dk|none))", x, value=TRUE, perl=TRUE)
## => [1] "business_metric_one" "business_metric_two"
See the R demo
The metric(?!.*(?:_dk|_none)) pattern matches
metric - a metric substring
(?!.*_(?:dk|none)) - that is not followed with any 0+ chars other than line break chars followed with _ and then either dk or none.
See the regex demo.
NOTE: if you need to match only such values that contain metric and do not end with _dk or _none, use a variation, metric.*$(?<!_dk|_none) where the (?<!_dk|_none) negative lookbehind fails the match if the string ends with either _dk or _none.
You can also do something like this:
grep("^([[:alpha:]]+_){2}[[:alpha:]]+$", string, value = TRUE)
# [1] "business_metric_one" "business_metric_two"
or use grepl to match dk and none, then negate the logical when you're indexing the original string:
string[!grepl("(dk|none)", string)]
# [1] "business_metric_one" "business_metric_two"
more concisely:
string[!grepl("business_metric_[[:alpha:]]+_(dk|none)", string)]
# [1] "business_metric_one" "business_metric_two"
Data:
string = c("business_metric_one","business_metric_one_dk","business_metric_one_none","business_metric_two","business_metric_two_dk","business_metric_two_none")
Here are some examples from my data:
a <-c("sp|Q9Y6W5|","sp|Q9HB90|,sp|Q9NQL2|","orf|NCBIAAYI_c_1_1023|",
"orf|NCBIACEN_c_10_906|,orf|NCBIACEO_c_5_1142|",
"orf|NCBIAAYI_c_258|,orf|aot172_c_6_302|,orf|aot180_c_2_405|")
For a: The individual strings can contain even more entries of "sp|" and "orf"
The results have to be like this:
[1] "sp|Q9Y6W5" "sp|Q9HB90,sp|Q9NQL2" "orf|NCBIAAYI_c_1_1023"
"orf|NCBIACEN_c_10_906,orf|NCBIACEO_c_5_1142"
"orf|NCBIAAYI_c_258,orf|aot172_c_6_302,orf|aot180_c_2_405"
So the aim is to remove the last "|" for each "sp|" and "orf|" entry. It seems that "|" is a special challenge because it is a metacharacter in regular expressions. Furthermore, the length and composition of the "orf|" entries varying a lot. The only things they have in common is "orf|" or "sp|" at the beginning and that "|" is on the last position. I tried different things with gsub() but also with the stringr package or regexpr() or [:punct:], but nothing really worked. Maybe it was just the wrong combination.
We can use gsub to match the | that is followed by a , or is at the end ($) of the string and replace with blank ("")
gsub("[|](?=(,|$))", "", a, perl = TRUE)
#[1] "sp|Q9Y6W5"
#[2] "sp|Q9HB90,sp|Q9NQL2"
#[3] "orf|NCBIAAYI_c_1_1023"
#[4] "orf|NCBIACEN_c_10_906,orf|NCBIACEO_c_5_1142"
#[5] "orf|NCBIAAYI_c_258,orf|aot172_c_6_302,orf|aot180_c_2_405"
Or we split by ,', remove the last character withsubstr, andpastethelist` elements together
sapply(strsplit(a, ","), function(x) paste(substr(x, 1, nchar(x)-1), collapse=","))
An easy alternative that might work. You need to escape the "|" using "\\|".
# Input
a <-c("sp|Q9Y6W5|","sp|Q9HB90|,sp|Q9NQL2|","orf|NCBIAAYI_c_1_1023|",
"orf|NCBIACEN_c_10_906|,orf|NCBIACEO_c_5_1142|",
"orf|NCBIAAYI_c_258|,orf|aot172_c_6_302|,orf|aot180_c_2_405|")
# Expected output
b <- c("sp|Q9Y6W5", "sp|Q9HB90,sp|Q9NQL2", "orf|NCBIAAYI_c_1_1023" ,
"orf|NCBIACEN_c_10_906,orf|NCBIACEO_c_5_1142" ,
"orf|NCBIAAYI_c_258,orf|aot172_c_6_302,orf|aot180_c_2_405")
res <- gsub("\\|,", ",", gsub("\\|$", "", a))
all(res == b)
#[1] TRUE
You could construct a single regex call to gsub, but this is simple and easy to understand. The inner gsub looks for | and the end of the string and removes it. The outer gsub looks for ,| and replaces with ,.
You do not have to use a PCRE regex here as all you need can be done with the default TRE regex (if you specify perl=TRUE, the pattern is compiled with a PCRE regex engine and is sometimes slower than TRE default regex engine).
Here is the single simple gsub call:
gsub("\\|(,|$)", "\\1", a)
See the online R demo. No lookarounds are really necessary, as you see.
Pattern details
\\| - a literal | symbol (because if you do not escape it or put into a bracket expression it will denote an alternation operator, see the line below)
(,|$) - a capturing group (referenced to with \1 from the replacement pattern) matching either of the two alternatives:
, - a comma
| - or (the alternation operator)
$ - end of string anchor.
The \1 in the replacement string tells the regex engine to insert the contents stored in the capturing group #1 back into the resulting string (so, the commas are restored that way where necessary).