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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 = ""; 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.

-- Ken

In reply to Re^3: Parsing problem by kcott
in thread Parsing problem by MB123

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