CODEWITHSUNDEEP
rstringdna-sequencesystemtime
Tomás Navarro
Tomás Navarro

Reputation: 170

Reading a file from a position in R

I have a large plain text file to be read in R, where all data is contained at the same line with no spaces (DNA sequence with no header). I found the next function:

readChar("filename",nchar=n)

which allows to read just the "n" first elements of the file saving a lot of time. Is there another function in R that goes further by reading just from START position to STOP one, avoiding to upload the whole file?

Upvotes: 1

Views: 581

Answers (2)

Sci Prog
Sci Prog

Reputation: 2691

You have to create a connexion, then use the seek function. Do not forget to close the connexion after.

For example, this will read 100 characters from position 1000.

cx <- file("filename", "rb")
seek(cx, 1000)
d <- readChar(cx, nchar=100)
close(cx)

Upvotes: 2

Ricardo Semi&#227;o
Ricardo Semi&#227;o

Reputation: 4456

Basically no, from what i know, you need to read the whole file and then discard the characters that you don't want. For example, if you want only the first 10 letters for every line:

strsub(readChar("filename",nchar=n),1,10)

But, this post (How to efficiently read the first character from each line of a text file?) shows some ways of improving the efficiency of that.

Upvotes: 1

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