perlquestion
MB123
<p>Hi all,</p>
I have this large text file in the format shown below -
<code> ID SNP
FT SNP 433
FT /note="refAllele: T SNPstrains: 7083_1#5=C 7414_8#8=C 7480_8#49=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
etc etc...</code>
And this code-<readmore>
<code>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 $out "Coordinate No of Strains AA Change";
my $SNP;
my $count;
my $change;
while ( my $line = <$in> ) {
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 $out "%-12.12s %-15.15s %s\n", $SNP, $count, $change;
}
}
}</code></p>
<p>However when I run the above code I receive a "Use of uninitialised value ($count or $change) in printf at Script.txt line 33 error. This occurs at any part of the text file that contains a non-synonymous mutation.</p>
<p>This code works on another text file I have, and the only difference I can see is that in this example file, strain numbers have a format such as 7521_5#39=A, whereas in the file this code worked for they are written as 7521_5_39=A, i.e. the '#' is replaced with a second '_'.</p>
<p>The ideal output from this code would look like this-</p>
<code>Coordinates No of Strains AA Change
703 1 AA Ala->Thr
937 1 AA Val->Leu
1804 3 AA Ser->Thr</code>
<p>Any help would be much appreciated, but please be advised I am very new to perl and programming in general. This code is also not my own work - a code that I had written suffered the same error.</p>
<p>Many thanks in advance!</P>
MB
</readmore>