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Help needed in feature extraction from two input files

arun 
Hi,
Try this:
lines1<- readLines("file1.txt")
lines1<- lines1[lines1!=""]
#In "file2.txt",
ATCGGATTCAGG
GAACCTATCGGGGGGGGAATTTA  
TATATTTTA###this should be a single line
ATCGGAGATATAACCAATC
AAAATTAACAAGAGAATAGACAAAAAAA
ATCTCTCTCCTCTCTCTCTAAAAA
ACGTGTGTACCCCC
#So, I modified the file manually so that it looks like:
ATCGGATTCAGG
GAACCTATCGGGGGGGGAATTTATATATTTTA
ATCGGAGATATAACCAATC
AAAATTAACAAGAGAATAGACAAAAAAA
ATCTCTCTCCTCTCTCTCTAAAAA
ACGTGTGTACCCCC

?#and saved.? If you have many lines showing the above mentioned anomaly, then let me know.

#I created a? new line after the last line (by using the `Enter` key) in the file to suppress the warnings() which I removed below.
lines2<- readLines("file2.txt")
lines2<- lines2[lines2!=""]


lines2New<-unlist(lapply(split(lines2,(seq_along(lines2)-1)%/%2+1),function(x) paste(x,collapse="\n")),use.names=FALSE)

##here changed because it was tab limited.
res<-lapply(lines1,function(x) {x1<- strsplit(x,"\t")[[1]]; x1New<-x1[-1];x2<-? gsub(">(.*)\\n.*","\\1",lines2New);lines3<-lines2New[match(x1New,x2)];write.table(lines3,paste0(x1[1],".txt"),row.names=FALSE,quote=FALSE)})


I didn't had any problems in the output.
It looks like below:
gene1.txt

x
ATCGGATTCAGG
ATCGGAGATATAACCAATC
ATCTCTCTCCTCTCTCTCTAAAAA

A.K.


Hi.. 

Thanks Arun, 

three output files are generated, but they show x and NA,, may be I have to check the input... 

and could u plz modify the script so that it will take ?direct input from files? I have attached the two input files.. 



----- Original Message -----
From: arun <smartpink111 at yahoo.com>
To: Utpal Bakshi <utpalmtbi at gmail.com>
Cc: R help <r-help at r-project.org>
Sent: Tuesday, June 11, 2013 2:52 PM
Subject: Re: Help needed in feature extraction from two input files

Hi,
Try this:
lines1<- readLines(textConnection("gene1 or1|1234 or3|56 or4|793
gene4 or2|347
gene5 or3|23 or7|123456789")) 


lines2<-readLines(textConnection(">or1|1234
ATCGGATTCAGG
GAACCTATCGGGGGGGGAATTTATATATTTTA
ATCGGAGATATAACCAATC
AAAATTAACAAGAGAATAGACAAAAAAA
ATCTCTCTCCTCTCTCTCTAAAAA
ACGTGTGTACCCCC"))?

lines2New<-unlist(lapply(split(lines2,(seq_along(lines2)-1)%/%2+1),function(x) paste(x,collapse="\n")),use.names=FALSE)


res<-lapply(lines1,function(x) {x1<- strsplit(x," ")[[1]]; x1New<-x1[-1];x2<-? gsub(">(.*)\\n.*","\\1",lines2New);lines3<-lines2New[match(x1New,x2)];write.table(lines3,paste0(x1[1],".txt"),row.names=FALSE,quote=FALSE)})


Attached is one of the files generated by the code.
A.K.


Hi all, 

I have two input files. First file (file1.txt) contains entries in the following tab delimited format: 

gene1??? or1|1234??? or3|56??? or4|793 
gene4??? or2|347 
gene5??? or3|23??? or7|123456789 

....... 
.. 


The second file (file2.txt) contains some additional features along with the header line of the first file, such as:
ATCGGATTCAGG
GAACCTATCGGGGGGGGAATTTA 
TATATTTTA
ATCGGAGATATAACCAATC
AAAATTAACAAGAGAATAGACAAAAAAA
ATCTCTCTCCTCTCTCTCTAAAAA
ACGTGTGTACCCCC 

.... 
..

Thread (2 messages)

arun Help needed in feature extraction from two input files Jun 11 arun Help needed in feature extraction from two input files Jun 11