MB123
Novice
Nov 29, 2012, 12:34 PM
Post #1 of 16
(7806 views)
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Script Advice: Is it doing what I think it is?
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Hi all,
I have these two scripts, which I have been using on an input file such as this:
FT SNP 467
FT /note="refAllele: C SNPstrains: 4330_2#1_EMRSA15=T 4330_2#5_EMRSA15=T 4340_5#9_EMRSA15=T 4340_6#3_EMRSA15=T 4340_6#4_EMRSA15=T 4350_2#2_EMRSA15=T 4350_2#3_EMRSA15=T 4386_1#4_EMRSA15=T 4386_2#12_EMRSA15=T 4386_2#5_EMRSA15=T "
FT /colour=1
FT SNP 522
FT /note="refAllele: G SNPstrains: 4330_8#2_EMRSA15=A (synonymous) 4340_5#2_EMRSA15=A (synonymous) 4340_6#8_EMRSA15=A (synonymous) 6133_2#2_EMRSA15=A (synonymous) 6133_2#4_EMRSA15=A (synonymous) "
FT /colour=3
FT SNP 523
FT /note="refAllele: G SNPstrains: 4414_6#1_EMRSA15=A (non-synonymous) (AA Glu->Lys) 6133_2#2_EMRSA15=A (non-synonymous) (AA Glu->Lys) "
FT /colour=2
FT SNP 546
FT /note="refAllele: G SNPstrains: 4350_1#3_EMRSA15=A (synonymous) 4386_5#5_EMRSA15=A (synonymous) 6133_1#11_EMRSA15=A (synonymous) ST398_EMRSA15=A (synonymous) "
FT /colour=3
use strict;
use warnings;
open( my $fh, '<', 'EARSS-MGE.txt') or die "Error opening file - $!\n";
open OUT, ">", "output.txt" or die "could not open output.txt $! \n";
my $this_line = "";
my $do_next = 0;
my $data = <DATA>;
while(<$fh>) {
my $last_line = $this_line;
$this_line = $_;
chomp $data;
if ($this_line =~ /\Q$data/) {
print OUT $last_line unless $do_next;
print OUT $this_line;
$do_next = 1;
} else {
print OUT $this_line if $do_next;
$last_line = "";
$do_next = 0;
}
}
close ($fh);
__DATA__
4386_7#8_
4350_7#6_
4414_1#6_
6133_2#2_
4465_5#1_
4465_5#6_
6236_1#3_
4330_8#8_
4386_6#1_
4414_5#9_
4340_5#10_
4340_6#11_
4386_6#8_
I believe that this one matches any one of the items under <DATA> and extracts that line, as well as the two immediately above and below it.
I have this second code:
use warnings;
use strict;
my %cod;
$cod{1} = "Int";
$cod{2} = "non";
$cod{3} = "syn";
$cod{4} = "stop";
$SIG{'__WARN__'} = sub{die $_[0]};
my $file = "Type 9.txt";
open IN, "<", $file or die "could not open $file $! \n";
open OUT, ">", "output.txt" or die "could not open output.txt $! \n";
print OUT "Coordinate No of Strains AA Change\n";
my $data = <DATA>;
my ($SNP, $count, $change);
while(<IN>){
if (m/^FT\s+SNP\s+(\d+)/) {
$SNP = $1;
}
elsif (m/^FT\s+\/note="(.*)"/) {
my $line = $1;
$count = ($line =~ tr/$data/$data/);
$line =~ m/\((AA \w+->\w+)\)\s*$/;
$change = $1 || "";
}
elsif (m/^FT\s+\/colour=(\d+)/) {
print OUT "$SNP $count $change\n" if $cod{$1} eq "non";
}
}
__DATA__
4386_7#8_
4350_7#6_
4414_1#6_
6133_2#2_
4465_5#1_
4465_5#6_
6236_1#3_
4330_8#8_
4386_6#1_
4414_5#9_
4340_5#10_
4340_6#11_
4386_6#8_
My main question is whether or not the count part of the second code "$count = ($line =~ tr/$data/$data/);" is working as I think - I am having a hard time telling from the output as some counts are ~500 which is difficult to go through by eye and see if any items not in <DATA> are included or not.
Also, does the use of '#' comment out the subsequent numbers in the items under <DATA>?
Any help would be greatly appreciated.
Many thanks
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