How to select names with wildcard from AAStringSet (biostrings)
Maybe a simple question, hopefully I get a simple answer.
I have imported a fasta file of proteins in R with biostrings.
> mySeqs <- readAAStringSet(fastaFile) # from package Biostrings
> mySeqs
A AAStringSet instance of length 318
width seq names
[1] 98 QVQLVQSGAEVKKPGASVKVSC...STAYMELRSLRSDDTAVYYCAR IGHV1-18*01
[2] 92 QVQLVQSGAEVKKPGASVKVSC...TTDTSTSTAYMELRSLRSDDTA IGHV1-18*02
[3] 98 QVQLVQSGAEVKKPGASVKVSC...STAYMELRSLRSDDMAVYYCAR IGHV1-18*03
[4] 98 QVQLVQSGAEVKKPGASVKVSC...STAYMELRSLRSDDTAVYYCAR IGHV1-18*04
[5] 98 QVQLVQSGAEVKKPGASVKVSC...STAYMELSRLRSDDTVVYYCAR IGHV1-2*01
... ... ...
[314] 91 QVQLVQSGSELKKPGASVKVSC...FSLDTSVSTAYLQISTLKAEDT IGHV7-4-1*03
[315] 98 QVQLVQSGSELKKPGASVKVSC...SMAYLQISSLKAEDTAVYYCAR IGHV7-4-1*04
[316] 98 QVQLVQSGSELKKPGASVKVSC...SMAYLQISSLKAEDTAVCYCAR IGHV7-4-1*05
[317] 98 QVQLVQSGHEVKQPGASVKVSC...STAYLQISSLKAEDMAMYYCAR IGHV7-81*01
[318] 98 EAQLTESGGDLVHLEGPLRLSC...YMLYMQMISLRTQNMAAFNCAG IGHV8-51-1*02
So how can I select only sequences with a certain name, lets say all names that contain "IGHV1". I have tried some grep, but that does not work on these objects.
Thanks in advance.
2 answers
Try:
mySeqs[grepl("IGHV1", mySeqs@ranges@NAMES)]
Example:
> mySeqs
A AAStringSet instance of length 10
width seq names
[1] 44 QVQLVQSGAEVKKPGASVKVSCSTAYMELRSLRSDDTAVYYCAR IGHV1-18*01
[2] 44 QVQLVQSGAEVKKPGASVKVSCTTDTSTSTAYMELRSLRSDDTA IGHV1-18*02
[3] 44 QVQLVQSGAEVKKPGASVKVSCSTAYMELRSLRSDDMAVYYCAR IGHV1-18*03
[4] 44 QVQLVQSGAEVKKPGASVKVSCSTAYMELRSLRSDDTAVYYCAR IGHV1-18*04
[5] 44 QVQLVQSGAEVKKPGASVKVSCSTAYMELSRLRSDDTVVYYCAR IGHV1-2*01
[6] 44 QVQLVQSGSELKKPGASVKVSCFSLDTSVSTAYLQISTLKAEDT IGHV7-4-1*03
[7] 44 QVQLVQSGSELKKPGASVKVSCSMAYLQISSLKAEDTAVYYCAR IGHV7-4-1*04
[8] 44 QVQLVQSGSELKKPGASVKVSCSMAYLQISSLKAEDTAVCYCAR IGHV7-4-1*05
[9] 44 QVQLVQSGHEVKQPGASVKVSCSTAYLQISSLKAEDMAMYYCAR IGHV7-81*01
[10] 44 EAQLTESGGDLVHLEGPLRLSCYMLYMQMISLRTQNMAAFNCAG IGHV8-51-1*02
> mySeqs[grepl("IGHV1", mySeqs@ranges@NAMES)]
A AAStringSet instance of length 5
width seq names
[1] 44 QVQLVQSGAEVKKPGASVKVSCSTAYMELRSLRSDDTAVYYCAR IGHV1-18*01
[2] 44 QVQLVQSGAEVKKPGASVKVSCTTDTSTSTAYMELRSLRSDDTA IGHV1-18*02
[3] 44 QVQLVQSGAEVKKPGASVKVSCSTAYMELRSLRSDDMAVYYCAR IGHV1-18*03
[4] 44 QVQLVQSGAEVKKPGASVKVSCSTAYMELRSLRSDDTAVYYCAR IGHV1-18*04
[5] 44 QVQLVQSGAEVKKPGASVKVSCSTAYMELSRLRSDDTVVYYCAR IGHV1-2*01
>
With a dummy dataset:
require(Biostrings)
example.dna <- DNAStringSet(c(`IGHV1-18*01`="ACGGTTAGT",
`IGHV1-18*02`="GTCGGGATA",
`IGHV2-18*03`="GGGTCTAAA"))
example.aa <- translate(example.dna)
## Make a named list of AAStrings, then combine to AAStringSet:
out.aa <- AAStringSet(x = sapply(grep("IGHV1", names(example.aa)),
function(x) {
tmp <- list(example.aa[[x]])
names(tmp) <- names(example.aa)[x]
return(tmp)
})
)
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