I would please like some help with this command because I didn't find anything in documentation that can cover everything I want.

I have some variables that are global, so I would prefer to keep them out of awk.

    outfile="exons_chr.bed" -> which should be composed according to chr,
                               so: "exons_" $chr ".bed"

and I want to apply awk in a general form,so that, for any "chr" input by user and any "infile", I could have a one-line command to just create an output according to following condition:

    awk '$1=="$chr" $infile > "exons_"$chr".bed"

So, I also want to compose the output filename each time. When I run it with specific values it works. How can I make it work with variables, to be more general,so that I can use it in a script ?

Is there a way to do it in more lines maybe, like :

    awk ' { if ($1=="$chr") -> copy lines to outfile }' infile
  • @Can you please provide some cod snippets of what are you doing like: Sample input, sample transformation, sample output? It is not clear for me what are you doing atm. – vfbsilva Mar 18 '15 at 13:39
  • @vfbsilva : I wanted to extract the lines of my Infile according to their first column which would be "chr10" or another "chr[1,2 etc] and save it to another file directly. But the syntax of awk with the variables as input was confusing me! Janis response is just what I needed ! :-) – MariaK Mar 19 '15 at 15:13

You have various options...

To pass shell variables to awk and use them in string comparison and let the shell create the file:

awk -v chr="$chr" '$1==chr' "$infile" > "exons_${chr}.bed"

To additionally let awk do the output into the file:

awk -v chr="$chr" '$1==chr { print > "exons_" chr ".bed" }' "$infile"
  • Thanx !! Both working very quickly ! ;-) – MariaK Mar 19 '15 at 15:13
  • On the same way but little more complex, I want to use while loop and & awk inside with variables in awk,as before. I opened a new Question for this : [ unix.stackexchange.com/questions/191400/… ], so @Janis, I would appreciate your help again, if you could! – MariaK Mar 20 '15 at 11:01

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