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 :)

In reply to How to continue numbering after a regular expression has been found by jpoldot

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