extracting columns with awk

gav251 · 03-09-2011, 07:25 AM

hi
why does this only use column 3?

awk '{print $3 $6 $7 >> "area.plt" }' mol.are
thnx.
g.

jschiwal · 03-09-2011, 07:29 AM

How are we supposed to know what .plt and .are files are.

Also, the >> "area.plt" part should be outside the awk command. Otherwise we can't tell you what the output would look like without a sample of the input.

Reuti · 03-09-2011, 07:39 AM

Quote:

Originally Posted by jschiwal

Also, the >> "area.plt" part should be outside the awk command.

According to man awk it's allowed to be used as option to a print command. Mabye it's a gawk extension.

But of course, w/o knowing the input we can't say much.

jschiwal · 03-09-2011, 07:44 AM

Thanks Reuti. I didn't know that. It does look strange, and I don't see why you would unless you are running an actual awk script.

colucix · 03-09-2011, 08:14 AM

Quote:

Originally Posted by jschiwal

I don't see why you would unless you are running an actual awk script.

Actually it is useful only when you have multiple redirections (to different files) inside the awk script or when the file name is built dinamycally under certain conditions.

@gav251: please follow the advice in the previous posts and show us the content (or just a sample) of the input file. Don't forget to embed it in CODE tags to preserve spacing and tabs (since they might be important to solve the puzzle). To use CODE tags, either put [CODE] and [/CODE] around the text or switch to advanced mode and press the # button.

gav251 · 03-10-2011, 05:52 AM

The .plt file is a new file, > would be ok. .mol file is a large file containing mathematical data about a proteins geometry. I didn't post it since the data is irrelevant. I just need to redirect columns 3, 6 and 7. Sorry for the ambiguity.
g.

Reuti · 03-10-2011, 06:24 AM

Quote:

Originally Posted by gav251

I didn't post it since the data is irrelevant. I just need to redirect columns 3, 6 and 7.

Obviously it's not irrelevant, otherwise your awk command would work. So showing one line of the input and the result which is produced by this line would allow to investigate the behavior.

colucix · 03-10-2011, 08:40 AM

Quote:

Originally Posted by Reuti

Obviously it's not irrelevant, otherwise your awk command would work. So showing one line of the input and the result which is produced by this line would allow to investigate the behavior.

The same from me. The result from such a simple code should be obvious, so most likely the problem resides in the input format: separators, hidden characters and so on. Please post a line of input, the corresponding output (as suggested above) plus the output of the following:

Code:

head -3 file.mol | od -c

and please use CODE tags.