[SOLVED] Maintain newline in grep's output

gigiux · 05-22-2018, 01:03 PM

Hello,

I am parsing a file using grep and the output on screen contains newline, as here:

Code:

    $ grep 'gene' sequence.gb
         gene            89..1483
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
         gene            complement(1987..2763)
                         /gene="nucleocapsid protein"
                         /gene="nucleocapsid protein"

I can assign this to a variable and print out still with the newlines:

Code:

    $ gene=$(grep 'gene' sequence.gb)
    echo "$gene"
         gene            89..1483
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
         gene            complement(1987..2763)
                         /gene="nucleocapsid protein"
                         /gene="nucleocapsid protein"

but this does not contain real newlines, since if I grep again for the lines containing '..' I get the whole lot:

Code:

    $ echo "$gene" | grep '..'
         gene            89..1483
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
                         /gene="non-structural protein"
         gene            complement(1987..2763)
                         /gene="nucleocapsid protein"
                         /gene="nucleocapsid protein"

We can see that this is a single string by not using the quotes:

Code:

    $ echo $gene
    gene 89..1483 /gene="non-structural protein" /gene="non-structural protein" /gene="non-structural protein" /gene="non-structural protein" /gene="non-structural protein" /gene="non-structural protein" /gene="non-structural protein" gene complement(1987..2763) /gene="nucleocapsid protein" /gene="nucleocapsid protein"

So my question is, how can I maintain newline formatting or introducing it?

Thank you

MadeInGermany · 05-22-2018, 02:54 PM

The newlines are there.
But .. in grep means two any-characters. Gets every line with two or more characters.
You need \.\. or [.][.] to match literal ..

gigiux · 05-23-2018, 02:28 PM

I completely forgot about the regex issue

. Of course it does, thank you! Now it is, as I wanted:

Code:

$ echo "$gene" | grep '\.\.'
gene            89..1483
gene            complement(1987..2763)