Re^6: compare lines within a file

The line

if ($row->[0] =~ m{\QHWUSI-EAS95L_0025_FC:3:1:5232:1082#0//E}) {

should have read

if ($row->[0] =~ m{\QHWUSI-EAS95L_0025_FC:3:1:5232:1082#0/\E}) {

There is a typo in the original code with an incorrect slash before the trailing E. The escaped pair \Q and \E tells Perl (when interpolating) to escape all characters that have special meaning in a regular expression - see Quote and Quote like Operators in perlop. The typo was of course mine, and I have corrected the original post accordingly. With that change, I get the output: 1449586 1449577. Obviously, you should be modifying that matching condition to fit your requirements.

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Re^7: compare lines within a file by garyboyd (Acolyte) on Mar 15, 2011 at 10:19 UTC
Thanks kennethk, this works, but I cannot figure out how to incorporate this into a program that can take a list and then check each line of the list to see if subsequent entries compare and if they do to then print out. It is possible to do this if the name is specified in the code `if ($row->[0] =~ m{\QHWUSI-EAS95L_0025_FC:3:1:5232:1082#0/\E}) {` but how to do this if you do not know what each line is?? I tried using the following regex, which will match each line: `if ($header2 =~ m{HWUSI-EAS95L_0025_FC:3:1:\d:\d#0/}) {` but not sure how to take it from there.....	[reply] [d/l] [select]
Re^8: compare lines within a file by kennethk (Abbot) on Mar 15, 2011 at 14:52 UTC
My general approach in this type of situation is to build a hash, or more specifically a hash of lists. I am not familiar with your particular input, and figuring out the patterns and how to parse them is usually where most of the effort in writing a script of this type falls. Taking the input from your original post: `HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/1 - 1449586 1449619 HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/2 - 1449544 1449577 HWUSI-EAS95L_0025_FC:3:1:6417:1078#0/1 - 4744083 4744113 HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/1 - 4867122 4867157 HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/2 - 4866942 4866977 HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/1 + 1930232 1930266 HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/2 + 1930354 1930389` [download] And fitting the most general pattern that seems to match, I would use code like #!/usr/bin/perl use strict; use warnings; use Text::CSV; my @result; my $csv = Text::CSV->new ( { sep_char => "\t" } ) # should set binary + attribute. or die "Cannot use CSV: ".Text::CSV->error_diag (); my %result; while ( my $row = $csv->getline( *DATA ) ) { my ($key, $index) = $row->[0] =~ m{^(.+)/([12])$} or die "Line did not match pattern: @$row"; if ($index == 1) { $result{$key}[0] = $row->[2]; } elsif ($index == 2) { $result{$key}[1] = $row->[2]; } else { die "Index was not 1 or 2: @$row" } } $csv->eof or $csv->error_diag(); # Output results: for my $key (keys %result) { next unless $result{$key}[1]; print "$key:\t$result{$key}[0]\t$result{$key}[1]\n"; } __DATA__ HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/1 - 1449586 1449619 HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/2 - 1449544 1449577 HWUSI-EAS95L_0025_FC:3:1:6417:1078#0/1 - 4744083 4744113 HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/1 - 4867122 4867157 HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/2 - 4866942 4866977 HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/1 + 1930232 1930266 HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/2 + 1930354 1930389 [download] to get the output `HWUSI-EAS95L_0025_FC:3:1:6539:1083#0: 4867122 4866942 HWUSI-EAS95L_0025_FC:3:1:5232:1082#0: 1449586 1449544 HWUSI-EAS95L_0025_FC:3:1:10260:1083#0: 1930232 1930354` [download] Note that because of how tabs get mangled on this site, you'll need to click the download link in order to get the proper formatting in your clipboard.	[reply] [d/l] [select]
Re^9: compare lines within a file by garyboyd (Acolyte) on Mar 22, 2011 at 08:33 UTC
brilliant! thank you so much for your help kennethk	[reply]