Thanks, I guess I should use =~ I also removed the . What I want the line of script to do: when I find a file with the string'HybridViralBact' I wanted to count the number of lines in that file. I think my main error now is with the wc -l syntax. Ther error is.

Argument "3503 /outputMC38..." isn't numeric in subtraction (-) at Perl_Chimera_File_Summ.pl line 30. 


#!/usr/bin/perl -w

my $Num_Bact_Virus_Chimera=0;
my $Num_Bact_Bact_Chimera=0;
my $Num_Virus_Virus_Chimera=0;
my $outfile='MC38_ChimeraTable.txt';
my $MG_Num=1;

open(OUT, ">$outfile") || die "Can't open outputfile $!\n";

print OUT join("\t",qw (MG_Num Num_Bact_Virus_Chimeras Num_Bact_Bact_C
+himera
Num_Virus_Virus_Chimera), "\n") ;

while ($MG_Num <= 72) {

@files=</g/bork6/mende/MGSimulation/hybridcontigs/outputMC38/*.MG$MG_N
+um.*>;

foreach $file (@files) {

if ($file=~/HybridViralBactContigsList/){

$Num_Bact_Virus_Chimera=qx/wc -l $file/;
$Num_Bact_Virus_Chimera=$Num_Bact_Virus_Chimera-1;

}

if ($file=~/HybridOnlyBactContigsList/){

$Num_Bact_Bact_Chimera=qx/wc -l $file/;
$Num_Bact_Bact_Chimera=$Num_Bact_Bact_Chimera-1;
}

if ($file=~/HybridOnlyVirusContigsList/){

$Num_Virus_Virus_Chimera=qx/wc -l $file/;
$Num_Virus_Virus_Chimera=$Num_Virus_Virus_Chimera-1;
}

print OUT
join("\t",$MG_Num,$Num_Bact_Virus_Chimera,$Num_Bact_Bact_Chimera,$Num_
+Virus_Virus_Chimera,"\n");


}

}
$MG_Num=$MG_Num+1;

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In reply to Re^2: Help with pattern matching and calling wc -l by Anonymous Monk
in thread Help with pattern matching and calling wc -l by AWallBuilder

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