Re^3: Parsing problem

[kcott]

Here's exactly what I used to test your code and data:

#!/usr/bin/env perl

use strict;
use warnings;
use feature qw(say);

#my $file = "BSAC.pl";
my %cod = ( 1 => "red", 2 => "non", 3 => "green" );
#open my $in, "<", "$file";
#open my $out, ">", "output.txt";
say "Coordinate   No of Strains   AA Change";

my $SNP;
my $count;
my $change;
while ( my $line = <DATA> ) {
    chomp $line;
    #say qq(DEBUG: Line = "$line");
    if ( $line =~ /^FT\s+SNP\s+(\d+)/ ){
        $SNP = $1;
        #say qq(\$SNP = $1;);
    }
    elsif ( $line =~ /^FT\s+\/note="(.*)"/) {
        my $note = $1;
        #say qq(my \$note = $1);
        $count = ($note =~ tr/=/=/);
        $note =~ /\((AA \w+->\w+)\)\s*$/;
        $change = $1 || "";
    }
    elsif ( $line =~ /^FT\s+\/colour=(\d+)/ ) {
        #say qq(Code = $1);
        if ( $cod{$1} eq "non" ) {
            printf "%-12.12s %-15.15s %s\n",  $SNP, $count, $change;
        }
    }
}

__DATA__
 ID  SNP
FT  SNP 433
FT      /note="refAllele: T SNPstrains: 7083_1#5=C 7414_8#8=C 7480_8#4
+9=C "
FT      /colour=1
FT  SNP 442
FT      /note="refAllele: T SNPstrains: 7065_8#2=C 7065_8#94=C 7083_1#
+2=C 7083_1#3=C 7083_1#41=C 7083_1#42=C 7083_1#43=C "
FT      /colour=1
FT  SNP 460
FT      /note="refAllele: T SNPstrains: 7564_8#14=C "
FT      /colour=1
FT  SNP 703
FT      /note="refAllele: G SNPstrains: 7521_5#39=A (non-synonymous) (
+AA Ala->Thr) "
FT      /colour=2
FT  SNP 937
FT      /note="refAllele: G SNPstrains: 7414_8#30=T (non-synonymous) (
+AA Val->Leu) "
FT      /colour=2
FT  SNP 1269
FT      /note="refAllele: G SNPstrains: 7480_7#22=A (synonymous) 7480_
+7#62=A (synonymous) "
FT      /colour=3
FT  SNP 1804
FT      /note="refAllele: T SNPstrains: 7414_7#66=A (non-synonymous) (
+AA Ser->Thr) 7414_8#44=A (non-synonymous) (AA Ser->Thr) 7521_6#54=A (
+non-synonymous) (AA Ser->Thr) "
FT      /colour=2

Try running this. Assuming it works, try changing the data to something you know will generate the warnings - keeping the data to an absolute minimum.

If you are also unable to reproduce the warnings, then the problem may lie in your input file. There might be embedded characters that aren't showing up when the text is copied and pasted. Anyway, I'm jumping the gun a bit here - see how you go with above code first.

[MB123]

Using your exact code and the data posted here, I get "Coordinates No of Strains AA Change" printed in my command line, and no output file created.

I don't understand how I am getting different results!

[kcott]

I now have some inkling of what the problem might be. I suspect you're missing some very fundamental knowledge. Don't panic about this: none of us was born with this information and you just haven't learned it yet. I can probably take you through this step-by-step but first I'll need some information. Please type

perl -v

at your command prompt and then post the full output (within <code>...</code> tags). Here's an example from my system (my command prompt is "$" - you don't type this):

$ perl -v

This is perl 5, version 14, subversion 2 (v5.14.2) built for darwin-th
+read-multi-2level

Copyright 1987-2011, Larry Wall

Perl may be copied only under the terms of either the Artistic License
+ or the
GNU General Public License, which may be found in the Perl 5 source ki
+t.

Complete documentation for Perl, including FAQ lists, should be found 
+on
this system using "man perl" or "perldoc perl".  If you have access to
+ the
Internet, point your browser at http://www.perl.org/, the Perl Home Pa
+ge.

[MB123]

I suspect I am missing a lot of fundamental knowledge! Here is my output -

This is perl 5, version 16, subversion 1 (v5.16.1) built for MSWin32-x
+64-multi-thread

Copyright 1987-2012, Larry Wall

Perl may be copied only under the terms of either the Artistic License
+ or the GNU General Public License, which may be found in the Perl 5 
+source kit.

Complete documentation for Perl, including FAQ lists, should be found 
+on this system using "man perl" or "perldoc perl". If you have access
+ to the Internet, point your browser at http://www.perl.org/, the Per
+l Home Page.