How to continue numbering after a regular expression has been found

jpoldot has asked for the wisdom of the Perl Monks concerning the following question:

Hello, I have a file starting with:

fixedStep chrom=chrX start=1 step=1 0.930

0.955

0.972

0.985

0.993

0.995

0.994

0.990

0.984

0.971

0.942

0.944

0.971

fixedStep chrom=chrX start=200 step=1

0.987

The problem is that, apart from the numbers shown, there are these headers found in the file multiple times. I want to construct a program that stores the position and the value, that means:

1 0.930

2 0.955

etc

the numbering starts from where it is indicated by the number stored in the field start, that is start = 200 etc...So this means:

200 0.987

etc

I have constructed the following code:

  
#!/usr/bin/perl -w

print "Please enter the filename of your file: ";
$dnafilename = <STDIN>;
chomp $dnafilename;

unless ( -e $dnafilename) {

    print "File \"$dnafilename\" doesn't seem to exist!!\n";
    exit;
}

unless ( open(DNAFILE, $dnafilename) ) {

    print "Cannot open file \"$dnafilename\"\n\n";
    exit;
}
while ( <DNAFILE> ) {
            
            next if (/fixedStep chrom=chrX start=(.+) step=1/);
            $counter = $1;
             
            }
             print "$counter\t$_\n";
            
close DNAFILE;


exit;
[download]

With awk, we could do it easily with the command: nawk -F' =' 'NF>1{start=$5;next}{print start++,$0}' myFile but I need a program...Any help would be greatly appreciated :)

Comment on How to continue numbering after a regular expression has been found Download Code

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Re: How to continue numbering after a regular expression has been found by jethro (Monsignor) on Feb 11, 2011 at 12:30 UTC
Your assignment to $counter is never executed at the right time because you do a next before it gets encountered. And if the 'if' is false, there shouldn't be an assignement to $counter but an increment. You probably want this: `while ( <DNAFILE> ) { if (/fixedStep chrom=chrX start=(.+) step=1/) { $counter = $1; next; } print "$counter\t$_\n"; $counter++; close DNAFILE;` [download] Code is untested.	[reply] [d/l]
Re^2: How to continue numbering after a regular expression has been found by jpoldot (Initiate) on Feb 11, 2011 at 12:49 UTC
Thank you very much...This works for me...Is there any way that I can store all these values into 2 arrays, one having the counter and the other the corresponding actual values???	[reply]
Re^3: How to continue numbering after a regular expression has been found by Ratazong (Monsignor) on Feb 11, 2011 at 13:01 UTC
There is even an easy way :-) push the `$counter` to one array and the `$_` to another instead of (or after the) `print` Rata	[reply] [d/l] [select]
Re: How to continue numbering after a regular expression has been found by Ratazong (Monsignor) on Feb 11, 2011 at 12:21 UTC
`while ( <DNAFILE> ) { next if (/fixedStep chrom=chrX start=(.+) step=1/); $counter = $1; } print "$counter\t$_\n";` [download] There are some issues with your code: if you find a heading-line, you leave the loop - the assignment `$counter = $1` will not be executed in this case according to your spec you want to print all non-heading-lines => the `print` needs to be inside the loop you want to increase the counter with your lines => you need a statement line `$counter++;` somewhere The following code might help you (untested!!) `while ( <DNAFILE> ) { if (/fixedStep chrom=chrX start=(.+) step=1/) { $counter = $1; } else { print "$counter\t$_\n"; $counter++; } }` [download] as you see, it is quite similar to your awk-code. HTH, Rata	[reply] [d/l] [select]