hello all, I have written a small subroutine and there seems to be some error in passing my variables to the subroutine. I am probably making an easy mistake in syntax, or it has to do with scope and private variables etc? Any help would be appreciated. Below is the part of the script related to the subroutine. In the subroutine the variable $proph is now =1 ?. 
########### subroutine get host and taxid ###
sub getDetails {
        my $proph=@_;
        my $host;my $taxid;my $genNum_proph;
        print "$proph\tproph inside sub";
        my @proph_columns=split(/\_/,$proph);
        # get host info
        if ($proph_columns[0] =~ /^FP92/){
                $host=$proph_columns[0];
        }
        else {
                $host=join("_",$proph_columns[0],$proph_columns[1]);
        }
        if ($host =~ /^NZ/){ ## for wgs genomes just match first 7 cha
+racters as only NZ_XXXX000000 are in tax2locus
                my $host=substr $host, 0, 7;
        }
        print "$host\t";
        #get taxid
        my ($matching_key)= grep { /^$host/  } keys %tax2loc;
        $taxid=$tax2loc{$matching_key};

        ## get number of proteins in the prophage
        if (exists $genesPerProphGen{$proph}){
                $genNum_proph=$genesPerProphGen{$proph};
        }
        else{
                print "$proph doesn't have number of genes\n"
        }

        return($host,$taxid,$genNum_proph);
}
##### Now make table with numbers #####

my $shared_table="$mci_file.sharedTab";
my $genNum_prophA;my $genNum_prophB;my $host_prophA;my $host_prophB;
open (OUTs,">$shared_table");
print OUTs "# This table was generated using $0 on\t".scalar(localtime
+(time))."\n";
print OUTs "#".join("\t",qw(Proph_genomeA Proph_genomeB hostA taxidA h
+ostB taxidB Jacc Prots_Shared Protsin_prophA Protsin_prophB))."\n";

foreach my $prophA (keys %$overlap){
        print "$prophA\tfrom overlap\t";
        my($hostA,$taxidA,$genNum_prophA)=&getDetails($prophA);
        foreach my $prophB (keys %{$overlap->{$prophA}}){
                my($hostB,$taxidB,$genNum_prophB)=&getDetails($prophB)
+;
                my $A_notShared=$genNum_prophA-$overlap->{$prophA}{$pr
+ophB};
                my $B_notShared=$genNum_prophB-$overlap->{$prophA}{$pr
+ophB};
                my $Jac_denom=$overlap->{$prophA}{$prophB}+$A_notShare
+d+$B_notShared;
                my $Jac=$overlap->{$prophA}{$prophB}/$Jac_denom;
                print OUTs join("\t",$prophA,$prophB,$host_prophA,$tax
+idA,$host_prophB,$taxidB,$Jac,$overlap->{$prophA}{$prophB},$genNum_pr
+ophA,$genNum_prophA)."\n";
        }
}
close(OUTs);

[download]
FP929058_PFPR05 from overlap    1       proph inside sub1_      1 does
+n't have number of genes

[download]

In reply to passing variables to a subroutine by AWallBuilder

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