Esteemed colleagues: I have written a little program to extract relevant lines out of data files and format them nicely, as shown: 

#!/usr/bin/perl
use warnings;
use strict;

# Formats a PennCNV output file to remove extraneous information. Also
+ removes
# CNVs containing less than 5 consecutive SNPs. Invoke this program wi
+th the name 
# of the file to be modified.

# Open input file and create output file, adding suffix '.truncated' t
+o filename:
open( my $file, '<', $ARGV[0] ) or die "Cannot open for reading, $!";
open( my $out, '>', $ARGV[0] . '.truncated' )
  or die "Cannot open for writing, $!";

# Print headings to output file:
printf $out "%-28s %-30s %-12s %-10s %-18s %-22s %-21s %s \n\n", "Samp
+le I.D.",
"Chromosome & coordinates", "Copy number", "No. SNPs", "CNV length (bp
+)", "First SNP", "Last SNP", "Overlapping Gene(s)";

# Loop that matches each valid line of input file, using capturing par
+entheses to
# isolate each separate field. We also use '/x' flag to allow arbitrar
+y whitespace
# so we can break the regular expression up and add comments for reada
+bility:
while (<$file>) {
    if (
/
(chr\d+:\d+-\d+)     # $1    Chromosome & coordinates
\s+
(numsnp=\d+)        # $2    Number of SNPs
\s+
(length=\S+)        # $3    CNV length (bp)
\s+
(state\d+)        # $4    HMM state
,
(cn=\d+)        # $5    Copy number
\s+
(\S+)                # $6    File directory
\/
(\S+)            # $7    Sample I.D.
\s+
(startsnp=rs\d+)    # $8    First SNP in CNV
\s+
(endsnp=rs\d+)        # $9    Last SNP in CNV
\s+
(\S+)            # $10    Gene(s) overlapping CNV
\s+
(\S+)            # $11    Distance of gene(s) from CNV
/x

       and ( !/numsnp=[1-4]\s+/ )  # we also ignore CNVs with less tha
+n 5 SNPs

       ) {
# Print each line to output file using left-justified formatting:
printf $out "%-28s %-30s %-12s %-10s %-18s %-22s %-21s %s \n",
             $7, $1, $5, $2, $3, $8, $9, $10;
    }
}

# Close the open filehandles:
close($file);
close($out);

[download]

My problem arises because I want to modify the program to write the rejected lines to a separate file, but when I try to use the capturing parentheses in an 'else' block inside the while loop right after the 'if', I end up with a blank file and perl gives me lots of errors relating to the $1, $2 etc. being out of scope.

So I'd like to know if there's an easy way of diverting any lines that don't match the 'if' patterns into a separate file.

Also, if anyone can spot other potential issues with my code, I'd appreciate constructive criticism. Thanks.

In reply to Capturing parentheses out of scope by iangibson

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