CODEWITHSUNDEEP
r
user3741035
user3741035

Reputation: 2545

Combine strings separated by multiple lines

I have a set of strings which has an ID that starts with >. I would like to get the strings that follow each ID on one line, and not separate on multiple lines like they are now. The string can sometimes be separated on 1,2 or 3 lines.

fileName="hairpin"
conn=file(fileName,open="r")
linn=readLines(conn)
for (i in 1:length(linn)){
 print(linn[i])
}
close(conn)
head(linn)

[1] ">cel-let-7 MI0000001 Caenorhabditis elegans let-7 stem-loop" 
[2] "UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAAC"
[3] "UAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA"                     
[4] ">cel-lin-4 MI0000002 Caenorhabditis elegans lin-4 stem-loop" 
[5] "AUGCUUCCGGCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAUUGAUGCUUCACACCU"
[6] "GGGCUCUCCGGGUACCAGGACGGUUUGAGCAGAU

output

[1] ">cel-let-7 MI0000001 Caenorhabditis elegans let-7 stem-loop"  "UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA"                     
[4] ">cel-lin-4 MI0000002 Caenorhabditis elegans lin-4 stem-loop"  "AUGCUUCCGGCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAUUGAUGCUUCACACCUGGGCUCUCCGGGUACCAGGACGGUUUGAGCAGAU"

I found the solution in anothet website:

 awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < file.fa

Upvotes: 1

Views: 97

Answers (1)

G. Grothendieck
G. Grothendieck

Reputation: 269644

Try this:

g <- cumsum(grepl("^>", Lines)) # equals 1 for first group, 2 for second, etc.
unname(unlist(tapply(Lines, g, function(x) c(x[1], paste(x[-1], collapse = "")))))

giving:

[1] ">cel-let-7 MI0000001 Caenorhabditis elegans let-7 stem-loop"                                        
[2] "UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAACUAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA"
[3] ">cel-lin-4 MI0000002 Caenorhabditis elegans lin-4 stem-loop"                                        
[4] "AUGCUUCCGGCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAUUGAUGCUUCACACCUGGGCUCUCCGGGUACCAGGACGGUUUGAGCAGAU"

Note The input Lines is:

Lines <- c(">cel-let-7 MI0000001 Caenorhabditis elegans let-7 stem-loop",
"UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAAC",
"UAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA",
">cel-lin-4 MI0000002 Caenorhabditis elegans lin-4 stem-loop",
"AUGCUUCCGGCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAUUGAUGCUUCACACCU",
"GGGCUCUCCGGGUACCAGGACGGUUUGAGCAGAU")

Upvotes: 1

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