Using strsplit wid pipe separator in R [duplicate] - r

This question already has answers here:
How to strsplit using '|' character, it behaves unexpectedly?
(4 answers)
Closed 4 years ago.
I have a string called line as below.
"2015-07-22|06:43:44+0000|37e86ffa-dd28-450d-aa9a-3d6776a31337|dummy|t1|USA-4DTV-DEFAULT|USA|MV000375100000|Striking Distance|MOVIE|TMS|VIEWED_MOVIE|NA|NA|NA|NA|**"
I am trying to split it on the separator "|", as :
strsplit(line, "|")
But the output is a s below :
[1] "2" "0" "1" "5" "-" "0" "7" "-" "2" "2" "|" "0" "6" ":" "4" "3" ":"
[18] "4" "4" "+" "0" "0" "0" "0" "|" "3" "7" "e" "8" "6" "f" "f" "a" "-"
[35] "d" "d" "2" "8" "-" "4" "5" "0" "d" "-" "a" "a" "9" "a" "-" "3" "d"
[52] "6" "7" "7" "6" "a" "3" "1" "3" "3" "7" "|" "d" "u" "m" "m" "y" "|"
[69] "t" "1" "|" "U" "S" "A" "-" "4" "D" "T" "V" "-" "D" "E" "F" "A" "U"
[86] "L" "T" "|" "U" "S" "A" "|" "M" "V" "0" "0" "0" "3" "7" "5" "1" "0"
[103] "0" "0" "0" "0" "|" "S" "t" "r" "i" "k" "i" "n" "g" " " "D" "i" "s"
[120] "t" "a" "n" "c" "e" "|" "M" "O" "V" "I" "E" "|" "T" "M" "S" "|" "V"
[137] "I" "E" "W" "E" "D" "_" "M" "O" "V" "I" "E" "|" "N" "A" "|" "N" "A"
[154] "|" "N" "A" "|" "N" "A" "|" "*" "*"
It is not even recognizing the pipe separators.

Just needs to add to backslash before the bar:
strsplit(x, "\\|")
For example:
> x <- "Hello | Could you help me please?"
> strsplit(x, "\\|")
[[1]]
[1] "Hello " " Could you help me please?"

Related

How to split sp|O00602|FCN1_HUMAN with (|)

How to split this string?
sp|O00602|FCN1_HUMAN
to
[[1]]
[1]"sp","O00602","FCN1_HUMAN"
I used the following code
strsplit("sp|O00602|FCN1_HUMAN",split ="|")
However, the result I got is
[[1]]
[1] "s" "p" "|" "O" "0" "0" "6" "0" "2" "|" "F" "C" "N" "1" "_" "H" "U" "M" "A" "N"
What should I do?
You should use fixed= TRUE so that | is interpreted as a literal string, not as a regular expression:
strsplit("sp|O00602|FCN1_HUMAN",split ="|", fixed= TRUE)
The character "|" is a meta-character, so you need to escape it.
strsplit("sp|O00602|FCN1_HUMAN", split = "\\|")
#[[1]]
#[1] "sp" "O00602" "FCN1_HUMAN"

R: Create a vector with all Keyboard constants

I want to create a vector that contains every constant in a QWERTY keyboard. For now I have:
keyboard <- c(LETTERS, letters, 0:9)
I need to add an element to the vector containing all the symbols (e.g. #, !, ?, etc...) Is there an R constant (such as LETTERS for all upper case letters in the alphabet) that contains all the symbols? If not, is there a fast way of getting them without typing them one by one?
The ascii printable characters are represented by 32 through 126. We can generate that vector, convert to 'raw', then use a function to change to the actual characters. After that we just break the string into pieces.
strsplit(rawToChar(as.raw(32:126)), "")[[1]]
which gives
> strsplit(rawToChar(as.raw(32:126)), "")[[1]]
[1] " " "!" "\"" "#" "$" "%" "&" "'" "(" ")" "*" "+" "," "-" "."
[16] "/" "0" "1" "2" "3" "4" "5" "6" "7" "8" "9" ":" ";" "<" "="
[31] ">" "?" "#" "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L"
[46] "M" "N" "O" "P" "Q" "R" "S" "T" "U" "V" "W" "X" "Y" "Z" "["
[61] "\\" "]" "^" "_" "`" "a" "b" "c" "d" "e" "f" "g" "h" "i" "j"
[76] "k" "l" "m" "n" "o" "p" "q" "r" "s" "t" "u" "v" "w" "x" "y"
[91] "z" "{" "|" "}" "~"

what is a vector of single characters

I have the following function (from package seqinr):
translate(seq, frame = 0, sens = "F", numcode = 1, NAstring = "X", ambiguous = FALSE)
Shortly, it translates DNA sequences into protein sequences. I have problems with giving the seq argument. The documentation says:
seq = the sequence to translate as a vector of single characters in lower case letters
I store the DNA sequence in a data.frame (named here seq):
seq <- data.frame(geneSeq="ATGTGTTGGGCAGCCGCAATACCTATCGCTATATCTGGCGCTCAGGCTATCAGTGGTCAGAACACTCAAGCCAAAATGATTGCCGTTCAGACCGCTGCTGGTCGTCGTCAAGCTATGGAAATCATGAGGCAGACGAACATCCAGAATGCTGACCTATCGTTGCAAGCTCGAAGTAACCTTGAGAAAGCGTCCGCCGAGTTGACCTCACAGAACATGCAKAAGGTCCAAGCTATTGGGTCTATCCGAGCGGCTATCGGAGAAAGTATGCTTGAAGGTTCCTCAATGGACCGTATTAAGCGAGTCACAGAAGGACAGTTCATTCGGGAAGCCAATATGGTAACTGAGAACTATCGCCGTGACTACCAAGCAATCTTCGTACAGCAACTTGGTGGTACTCAAAGTGCTGCAAGTCAGATTGACGAAATCTATAAGAGCGAACAGAAACAGAAGAGTAAGCTACAGATGGTTCTGGACCCACTGGCTATCATGGGGTCTTCCGCTGCGAGTGCTTACGCATCCGATGCGTTCGACTCTAAGTTCACAACTAAGGCACCTATTGTTGCCGCTAAAGGAACCAAGACGGGGAGGTAA", stringsAsFactors=FALSE)
Every time I try to use the translate function, it returns the error:
Error in s2n(seq, levels = s2c("tcag")) :
sequence is not a vector of chars
I have tried the following, all give the above error:
trans<- seqinr::translate(tolower(seq[1,1]))
trans<- seqinr::translate(stringr::str_split(tolower(seq[1,1]), pattern=""))
trans<- seqinr::translate(as.character(stringr::str_split(tolower(seq[1,1]), pattern="")))
How can I transform my DNA sequence in a vector of single characters?
You could use strsplit:
strsplit("ABCD", "")
# [[1]]
# [1] "A" "B" "C" "D"
## your example:
seqinr::translate(strsplit(seq[1,1], "")[[1]])
The first example in ?translate pretty much gives you your answer.
You don't need a data frame and can use s2c whose sole purpose in life is for "conversion of a string into a vector of chars":
geneSeq="ATGTGTTGGGCAGCCGCAATACCTATCGCTATATCTGGCGCTCAGGCTATCAGTGGTCAGAACACTCAAGCCAAAATGATTGCCGTTCAGACCGCTGCTGGTCGTCGTCAAGCTATGGAAATCATGAGGCAGACGAACATCCAGAATGCTGACCTATCGTTGCAAGCTCGAAGTAACCTTGAGAAAGCGTCCGCCGAGTTGACCTCACAGAACATGCAKAAGGTCCAAGCTATTGGGTCTATCCGAGCGGCTATCGGAGAAAGTATGCTTGAAGGTTCCTCAATGGACCGTATTAAGCGAGTCACAGAAGGACAGTTCATTCGGGAAGCCAATATGGTAACTGAGAACTATCGCCGTGACTACCAAGCAATCTTCGTACAGCAACTTGGTGGTACTCAAAGTGCTGCAAGTCAGATTGACGAAATCTATAAGAGCGAACAGAAACAGAAGAGTAAGCTACAGATGGTTCTGGACCCACTGGCTATCATGGGGTCTTCCGCTGCGAGTGCTTACGCATCCGATGCGTTCGACTCTAAGTTCACAACTAAGGCACCTATTGTTGCCGCTAAAGGAACCAAGACGGGGAGGTAA"
print(translate(s2c(geneSeq), frame = 0, sens = "F", numcode = 1, NAstring = "X", ambiguous = FALSE)
## [1] "M" "C" "W" "A" "A" "A" "I" "P" "I" "A" "I" "S" "G" "A" "Q" "A" "I" "S" "G" "Q" "N" "T" "Q" "A" "K"
## [26] "M" "I" "A" "V" "Q" "T" "A" "A" "G" "R" "R" "Q" "A" "M" "E" "I" "M" "R" "Q" "T" "N" "I" "Q" "N" "A"
## [51] "D" "L" "S" "L" "Q" "A" "R" "S" "N" "L" "E" "K" "A" "S" "A" "E" "L" "T" "S" "Q" "N" "M" "X" "K" "V"
## [76] "Q" "A" "I" "G" "S" "I" "R" "A" "A" "I" "G" "E" "S" "M" "L" "E" "G" "S" "S" "M" "D" "R" "I" "K" "R"
## [101] "V" "T" "E" "G" "Q" "F" "I" "R" "E" "A" "N" "M" "V" "T" "E" "N" "Y" "R" "R" "D" "Y" "Q" "A" "I" "F"
## [126] "V" "Q" "Q" "L" "G" "G" "T" "Q" "S" "A" "A" "S" "Q" "I" "D" "E" "I" "Y" "K" "S" "E" "Q" "K" "Q" "K"
## [151] "S" "K" "L" "Q" "M" "V" "L" "D" "P" "L" "A" "I" "M" "G" "S" "S" "A" "A" "S" "A" "Y" "A" "S" "D" "A"
## [176] "F" "D" "S" "K" "F" "T" "T" "K" "A" "P" "I" "V" "A" "A" "K" "G" "T" "K" "T" "G" "R" "*"

How to search and isolate attributes of FASTA formatted text in R

I have a FASTA formatted file, which is essentially a special text file, containing many entries, one of which looks like below, which I have assigned by the name "FASTA" in R. The original file was red and formated as seen below using seqinr package in R.
FASTA<- structure(list(`tr|A1Z6G9|A1Z6G9_DROME` = structure("MSISASHPCGLNADGTATQYKESTATIQTSGLQSSPRSFLPEREDTLEYFIKFPKPSSKNEFVLAKDHDGEDSHVPIVMLLGWAGCQDRYLMKYSKIYEERGLITVRYTAPVDSLFWKRSEMIPIGEKILKLIQDMNFDAHPLIFHIFSNGGAYLYQHINLAVIKHKSPLQVRGVIFDSAPGERRIISLYRAITAIYGREKRCNCLAALVITITLSIMWFVEESISALKSLFVPSSPVRPSPFCDLKNEANRYPQLFLYSKGDIVIPYRDVEKFIRLRRDQGIQVSSVCFEDAEHVKIYTKYPKQYVQCVCNFIRNCMTIPPLKEAVNSEPSESVSRVNLKYD", name = "tr|A1Z6G9|A1Z6G9_DROME", Annot = ">tr|A1Z6G9|A1Z6G9_DROME CG8245 OS=Drosophila melanogaster GN=CG8245-RA PE=2 SV=1", class = "SeqFastaAA")))
Now although this format allows me to get the name indices of the entry/entries, when I search for it using grep, as seen below
grep("A1Z6G9_DROME", names(FASTA))
or isolate its name using
as.vector(sapply(names(attributes(FASTA)), function(x) attr(FASTA, x)))
However I can not either grep/regexpr any of the text/information in the attributes sections or isolate any of the attributes, such as the text following name= or Annot= section. Can anyone help me with this?
As far as I could gather, when googling read.fasta in R, the manual relating to the seqinr package states something along the lines of annotations/attributes being ignored (I think) but these attribute sections hold important information regarding the identity of the entry, which I desperately need! I have tried the unlist or collapse with the paste function but they remove all the attributes that I need!
There are a lot of get* functions in the seqinr package (see http://www.rdocumentation.org/packages/seqinr). These functions are designed to access different attributes, e.g.:
getAnnot(FASTA)
#[[1]]
#[1] ">tr|A1Z6G9|A1Z6G9_DROME CG8245 OS=Drosophila melanogaster GN=CG8245-RA PE=2 SV=1"
getSequence(FASTA)
#[[1]]
# [1] "M" "S" "I" "S" "A" "S" "H" "P" "C" "G" "L" "N" "A" "D" "G" "T" "A" "T" "Q" "Y" "K" "E" "S" "T" "A" "T" "I" "Q" "T" "S" "G" "L" "Q" "S" "S" "P" "R" "S" "F" "L" "P" "E" "R" "E" "D" "T" "L" "E" "Y" "F" "I" "K" "F" "P" "K" "P" "S" "S" "K"
# [60] "N" "E" "F" "V" "L" "A" "K" "D" "H" "D" "G" "E" "D" "S" "H" "V" "P" "I" "V" "M" "L" "L" "G" "W" "A" "G" "C" "Q" "D" "R" "Y" "L" "M" "K" "Y" "S" "K" "I" "Y" "E" "E" "R" "G" "L" "I" "T" "V" "R" "Y" "T" "A" "P" "V" "D" "S" "L" "F" "W" "K"
#[119] "R" "S" "E" "M" "I" "P" "I" "G" "E" "K" "I" "L" "K" "L" "I" "Q" "D" "M" "N" "F" "D" "A" "H" "P" "L" "I" "F" "H" "I" "F" "S" "N" "G" "G" "A" "Y" "L" "Y" "Q" "H" "I" "N" "L" "A" "V" "I" "K" "H" "K" "S" "P" "L" "Q" "V" "R" "G" "V" "I" "F"
#[178] "D" "S" "A" "P" "G" "E" "R" "R" "I" "I" "S" "L" "Y" "R" "A" "I" "T" "A" "I" "Y" "G" "R" "E" "K" "R" "C" "N" "C" "L" "A" "A" "L" "V" "I" "T" "I" "T" "L" "S" "I" "M" "W" "F" "V" "E" "E" "S" "I" "S" "A" "L" "K" "S" "L" "F" "V" "P" "S" "S"
#[237] "P" "V" "R" "P" "S" "P" "F" "C" "D" "L" "K" "N" "E" "A" "N" "R" "Y" "P" "Q" "L" "F" "L" "Y" "S" "K" "G" "D" "I" "V" "I" "P" "Y" "R" "D" "V" "E" "K" "F" "I" "R" "L" "R" "R" "D" "Q" "G" "I" "Q" "V" "S" "S" "V" "C" "F" "E" "D" "A" "E" "H"
#[296] "V" "K" "I" "Y" "T" "K" "Y" "P" "K" "Q" "Y" "V" "Q" "C" "V" "C" "N" "F" "I" "R" "N" "C" "M" "T" "I" "P" "P" "L" "K" "E" "A" "V" "N" "S" "E" "P" "S" "E" "S" "V" "S" "R" "V" "N" "L" "K" "Y" "D"

Letter "y" comes after "i" when sorting alphabetically

When using function sort(x), where x is a character, the letter "y" jumps into the middle, right after letter "i":
> letters
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" "t"
[21] "u" "v" "w" "x" "y" "z"
> sort(letters)
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "y" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"
[21] "t" "u" "v" "w" "x" "z"
The reason may be that I am located in Lithuania, and this is "lithuanian-like" sorting of letters, but I need normal sorting. How do I change the sorting method back to normal inside R code?
I'm using R 2.15.2 on Win7.
You need to change the locale that R is running in. Either do that for your entire Windows install (which seems suboptimal) or within the R sessions via:
Sys.setlocale("LC_COLLATE", "C")
You can use any other valid locale string in place of "C" there, but that should get you back to the sort order for letters you want.
Read ?locales for more.
I suppose it is worth noting the sister function Sys.getlocale(), which queries the current setting of a locale parameter. Hence you could do
(locCol <- Sys.getlocale("LC_COLLATE"))
Sys.setlocale("LC_COLLATE", "lt_LT")
sort(letters)
Sys.setlocale("LC_COLLATE", locCol)
sort(letters)
Sys.getlocale("LC_COLLATE")
## giving:
> (locCol <- Sys.getlocale("LC_COLLATE"))
[1] "en_GB.UTF-8"
> Sys.setlocale("LC_COLLATE", "lt_LT")
[1] "lt_LT"
> sort(letters)
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "y" "j" "k" "l" "m" "n"
[16] "o" "p" "q" "r" "s" "t" "u" "v" "w" "x" "z"
> Sys.setlocale("LC_COLLATE", locCol)
[1] "en_GB.UTF-8"
> sort(letters)
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o"
[16] "p" "q" "r" "s" "t" "u" "v" "w" "x" "y" "z"
> Sys.getlocale("LC_COLLATE")
[1] "en_GB.UTF-8"
which of course is what #Hadley's Answer shows with_collate() doing somewhat more succinctly once you have devtools installed.
If you want to do this temporarily, devtools provides the with_collate function:
library(devtools)
with_collate("C", sort(letters))
# [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"
# [20] "t" "u" "v" "w" "x" "y" "z"
with_collate("lt_LT", sort(letters))
# [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "y" "j" "k" "l" "m" "n" "o" "p" "q" "r"
# [20] "s" "t" "u" "v" "w" "x" "z"

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