Hi all,

I am trying to write a perl script that loops through the files in a directory. First I want to find all the files that have 'MG1' in the name, then I want to count the lines in three different files (based on the filename). I then want to loop through this until MG72. And output the data as a table.

I think I have a few errors. I'm not sure about the pattern matching for the file name, and I don't think I'm calling wc-l properly.

Any advice? thanks 


#!/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=</outputMC38/*.MG$MG_Num.*>;

foreach $file (@files) {

if ($file=qr/HybridViralBactContigsList.txt/){

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

}

if ($file=qr/HybridOnlyBactContigsList.txt/){

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

if ($file=qr/HybridOnlyVirusContigsList.txt/){

$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 Help with pattern matching and calling wc -l by AWallBuilder

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