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I tried to subset the dataframe in R since there are empty space after each line in the sequence which shows 'NA' when i read the files into R ,as a result of which when i subset it just takes the sequence Protein_IDS and sequence line by line not as whole

Im looking for this Protein_ID in one column and respective sequence in other 

Proteins_IDs                Sequence                                                    
  <chr>                       <chr>                                                       
1 fig|6666666.151743.peg.5284 MERQAVAVVFHDWRRAIQQRNKTAAADRGVDPVGVGHNSKIESLQPRSSVCRASLIQVPG
2 NA                          RLLNGEIFYSLAEAKVLIEAWRRHYNTVRPHSSLGYRPPAPETATPPYPASGSASLHLRP
3 NA                          DMAAMGLIH                                                   
4 NA                          NA                                                          
5 fig|6666666.151743.peg.5285 MIDRQTAQVRRWSFVLGSSIAAMAAASATPAWAQCSPDPTVADSVTNCTGTDSDGLRVTT
6 NA                          DGSMVEVAPSASVSGAGAAAITVDIAPVSGSYYARKATINVGGSVDGGTQSGISVLSGSV

So i have made another file with list of protein ID which i want to subset from this file..I tried removing empty space from the file but couldn;t as it the sequence should come in one line but instead there is line break

data files

I tried this SEQ <- inner_join(seq,protein_id) whose output is this its like each ID is associated with multiple sequence 

fig|6666666.151743.peg.5044 MTKNTIHRTILVCASLIAMPAMAQGTTEAGQEGASLADIVVTAQRRSENLQNVPISVTAI
2 fig|6666666.151743.peg.5063 MTVEQALARMLEGTGLEAQRLSPTAYRLVQAAPPASRRDPVRPAPPLPPEGSVDIIVTGT
3 fig|6666666.151743.peg.5135 MLRVADGYVEEAADDAIVPSPAVPLSVPSAPVRFEAAPARYGARRGPNVPAILVIVLLHA
kcm
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  • It is very hard to understand your question. Please try to formulate the question, by telling what you have, what you want and what you have tried (including code). – benn Nov 30 '18 at 12:02
  • edited the question – kcm Nov 30 '18 at 12:11

1 Answers1

5

I want to advise you to use FASTA format, instead of obscure unknown formats. In R, there are many packages that can handle FASTA format and it is therefore more convenient. I will show you how to make a FASTA file from your data, and then I will show an example of how to import such a FASTA file and sub select your proteins of interest.

input <- scan("seq2.txt", what = character(), sep = "\t")
length(input)
new <- gsub("f", ">f", input[-1:-2])
write.table(new, "seq2.fasta", quote = F, row.names = F, col.names = F)

library(seqinr)
fasta.file <- read.fasta("seq2.fasta", seqtype = "AA", as.string = TRUE)
prot.id <- scan("protein_id.txt", what = character(), sep = "\t")
selection <- fasta.file[names(fasta.file) %in% prot.id]
length(selection)
[1] 87

head(selection, 2)
$`fig|6666666.151743.peg.5044`
[1] "MTKNTIHRTILVCASLIAMPAMAQGTTEAGQEGASLADIVVTAQRRSENLQNVPISVTAITSEQAIKLGITQPDVIAQMVPGLQLNHSAWGLTPFLRGVGTNSVAIGNEPAVALFVDDVYLPTGSAGVFQLNSISSIEVLKGPQGTLFGRNATGGVIHIRTRDPSFDPSASATASYGNYDTISGQLYGSTGLTDTVAINFALQGIDQRKGWGVNGTTGNEANSMSGWGGRAKLLWNMGEETSLLVAGSYDRRSSDQGQPGRSIAGTFTRDGYSADAAGLGFYDVMSNLDTVQKSTTRSLSGKLTHDFGSARLVLISAFSKTVVDPVVSDSDGSPSPFFQTREFAMGGRTFTQEVQLLSPEGSAVKWILGAFYLHDRSFMDATYEGQAFGTSKSHTDAVQRTNSIAGFGQVTTEILPRTNLTLGLRYTSDRRSLDAVARLLPATGAAVTFGPFEDAKTFNSVTGRASIDHHFSDDLMGYIAYNRGFKSGIYNFTGIVAGTTTLPPPVNPETLDAYTIGFKSEFLNRRLRVNAEAFLYEYSDLQVQIVLPTGTTLTNASKATIKGIDFEISAIPVRNLTVSASIGLLDGRYKDFRNAPSFFLLPPNAPTPYDPARCSGPNPYPAVQGSAPATQRSCDVSGNRLIQAPPFSSNLQLLYTLPTDLGDFDLSASWAHGGNYEYDVFSSPLTRQPRTDIVNGSVQWTAPGGTFNVRLWANNLTGEKYYTIATTGSTAGAKYAAAAPRTYGVTLGANF"
attr(,"name")
[1] "fig|6666666.151743.peg.5044"
attr(,"Annot")
[1] ">fig|6666666.151743.peg.5044"
attr(,"class")
[1] "SeqFastaAA"

$`fig|6666666.151743.peg.5063`
[1] "MTVEQALARMLEGTGLEAQRLSPTAYRLVQAAPPASRRDPVRPAPPLPPEGSVDIIVTGTKREEPLARLPISVAIVQAPGEQGGALLPGTEEVAQRLDGLTLTNLGPGRNRQFIRGVADSPFNGNSQSTVAILINDARATYNAPDPDLKLVDVERVELLKGPQGSLYGTGTLGGVYHIVTRPPDAGSFAAMAGMGASLATHGEMGGSAEAMVNLPVVADRLALRAVAYAVREPGWIDTAGRGDANRGELRGGRVALRALAGDWTVDLNGMAQMRDVADSQYVYARHALERPAQPAEPHDNDFALMALRVAGKLGGADLVYAGNWVDHDVSSTLDASDLSASAFGIAPPALYLEQRRNRLFDQEVRLSQTRDDGLSWLAGLSFVDVRNHLSGVVRGVRDETVGTGIQGVVEFSAFGDMRMPLTGALSLSVGGRLFHSRIEEEQGARHARIEASVARSGFTPSLALSWQAGAHDFLYARYAGALRPGGLSRTGAASAERFESDELQTVEMGWRHSASAWLTVNLDAFLTTWSHMQSDYLLADGLIGTRNVGDARIRGVEASVDWKPAAGWAISAGLVGQSALLTRTNEGLRLEDRHLPVVPDWKARFGVNRHFDLSGWSGSMGVNLAYLGPSRLSFDPGLDRRMGDYALANADLALRRKDWSIRLSGSNLLDCKADSFAFGNPFALARGTQYTPLRPRQWAIGFTKNW"
attr(,"name")
[1] "fig|6666666.151743.peg.5063"
attr(,"Annot")
[1] ">fig|6666666.151743.peg.5063"
attr(,"class")
[1] "SeqFastaAA"
terdon
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benn
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  • looks like its bit more complicated than i thought let me run ,do you have a sed or awk ways to get around this file format? – kcm Nov 30 '18 at 13:54
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    No, like I said: I advice you to USE the fasta file format because you can use a lot of tools for your purposes instead of reinventing the wheel with your own format. – benn Nov 30 '18 at 13:58
  • how did you write the selection object into a file as the object is list .."Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ‘"SeqFastaAA"’ to a data.frame" – kcm Nov 30 '18 at 14:06
  • able to write it...and im really glad for your help..... – kcm Nov 30 '18 at 14:17
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    Great to hear, good luck with the analysis. – benn Nov 30 '18 at 16:28