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
>or2|347
GAACCTATCGGGGGGGGAATTTATATATTTTA
>or3|56
ATCGGAGATATAACCAATC
>or3|23
AAAATTAACAAGAGAATAGACAAAAAAA
>or4|793
ATCTCTCTCCTCTCTCTCTAAAAA
>or7|123456789
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:
>or1|1234
ATCGGATTCAGG
>or2|347
GAACCTATCGGGGGGGGAATTTA
TATATTTTA
>or3|56
ATCGGAGATATAACCAATC
>or3|23
AAAATTAACAAGAGAATAGACAAAAAAA
>or4|793
ATCTCTCTCCTCTCTCTCTAAAAA
>or7|123456789
ACGTGTGTACCCCC
....
..
From these two files, I want to extract entries by row wise
header matching and rename the output file as the first column in file1.
For example, in the above case, 3 output files will generate.
the first output file would named as "gene1.txt" and it contains:
>or1|1234
ATCGGATTCAGG
>or3|56
ATCGGAGATATAACCAATC
>or4|793
ATCTCTCTCCTCTCTCTCTAAAAA
the second output file would named as "gene4.txt" and it contains:
>or2|347
GAACCTATCGGGGGGGGAATTTATATATTTTA
the third output file would named as "gene5.txt" and it contains:
>or3|23
AAAATTAACAAGAGAATAGACAAAAAAA
>or7|123456789
ACGTGTGTACCCCC
Any help in solving the problem is highly appreciated. Thanks in advance. x
>or1|1234
ATCGGATTCAGG
>or3|56
ATCGGAGATATAACCAATC
>or4|793
ATCTCTCTCCTCTCTCTCTAAAAA
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