Read data into R deleting or skipping lines containing characters

Question

I'm sure this is simple, but I'm not coming across an answer. I would like to import a data frame into R without processing the lines in a text editor first. Essentially, I want R to do it on read in. So all lines containing

FRAME   1 of ***
OR
ATOM-WISE TOTAL CONTACT ENERGY

will be skipped, deleted or ignored.

And all that will be left is;

Chain Resnum    Atom number Energy(kcal/mol)
ATOM      C     500   1519          -2.1286
ATOM      C     500   1520          -1.1334
ATOM      C     500   1521          -0.8180
ATOM      C     500   1522          -0.7727

Is there a simple solution to this? I'm not sure which scan() of read.table() arguments would work.

EDIT

I was able to use readLines and gsub to read in the file and remove the (un)necessary lines. I omitted the "" left from the deleted words and now I am trying to convert the character df to a regular(numeric) df. When I use data.frame(x) or as.data.frame(x) I am left with a data frame with 100K rows and only one variable. There should be at least 5 variables.

Is it a speed issue? i.e. Why couldn't you delete these lines after import? — Marc in the box, Jun 16 '15 at 13:48
The text makes the data harder to work with. Deleting these lines would give me a numeric data frame which is what I want. — D.A. Ragland, Jun 16 '15 at 13:50
Can you give a bigger example of your file with the data and non-data lines? — Molx, Jun 16 '15 at 13:50
Use `readLines`, then `grepl` to exclude rows that match unwanted list of strings. Or you can run system command for `read.table`, see [this post](http://stackoverflow.com/questions/10690867/how-to-run-shell-script-in-r-and-get-the-output-into-table) — zx8754, Jun 16 '15 at 13:52
You can also convert to numeric once you delete those lines (`as.numeric`) — Marc in the box, Jun 16 '15 at 14:14
@D.A.Ragland this post is what you want, http://stackoverflow.com/questions/14261776/extracting-data-from-text-files it is even related to Molecular Modelling (but GAMESS (US)). — DarrenRhodes, Jun 16 '15 at 14:56

score 1 · Answer 1 · answered Jun 16 '15 at 19:02

readLines gives you a vector with one character string for each line of the file. So you have to split these strings into the elements you want before you convert to a dataframe. If you have nice space-separated values, try:

m = matrix(unlist(strsplit(data, " +")), ncol=5, byrow=TRUE)
    # where 'data' is the name of the vector of strings
df = data.frame(m, stringsAsFactors=FALSE)

Then for each column with numeric data, use as.numeric() on the column to convert.

YOU ARE A GOD SEND! THANK YOU VERY MUCH! – D.A. Ragland Jun 16 '15 at 19:08 — D.A. Ragland, Jun 16 '15 at 19:08

Read data into R deleting or skipping lines containing characters

1 Answers1