Re^2: help with hash or arrays or hash references

Great Thanks. I had just realized the that I had to move the declaration to outside of the if else loop. I also like the idea of a subroutine. Subroutine is now working. Here working code for any following this thread

new code

############### read in blast table and parse #######
my $in_blast_tab=$ARGV[0];
open(IN,$in_blast_tab) or die "cannot open $in_blast_tab\n";

my %HoFlg1; my %HoFlg2;
#my $Flag1; my $Flag2;

while (my $line=<IN>) {
        chomp $line;
        my ($Query_id,$strand,$Subj_id,$Perc_iden,$align_len,$num_mm,$
+gap,$q_start,$q_end,$s_start,$s_end,$e_value,$bit_score)=split("\t",$
+line); # extra field of strand
        next if ($bit_score <60);
        my ($Flag1, $Flag2 ) = &Flag( $Subj_id, \%proph_prots, \%euk_p
+rots, \%vir_prots );
        $HoFlg1{$Query_id}{$Subj_id}{$bit_score}=$Flag1;
        $HoFlg2{$Query_id}{$Subj_id}{$bit_score}=$Flag2;
        print join("\t",$Query_id,$Subj_id,$bit_score,$Flag1,$Flag2)."
+\n";
}

sub Flag {
        my $Subj_id=$_[0];
        my $proph_prots=$_[1];
        my $euk_prots=$_[2];
        my $vir_prots=$_[3];
        my $Flag1; my $Flag2;
        if (exists $proph_prots{$Subj_id}){
                $Flag1="Proph";
                $Flag2="Phage";
        }
        elsif (exists $euk_prots{$Subj_id}){
                $Flag1="Euk";
                $Flag2="Euk"
        }
        elsif(exists $vir_prots{$Subj_id}){
                $Flag1="Vir";
                $Flag2="Phage";
        }
        else {
                $Flag1="Bact";
                $Flag2="Bact";
        }
        return($Flag1,$Flag2);
}
[download]

Comment on Re^2: help with hash or arrays or hash references Download Code

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Re^3: help with hash or arrays or hash references by Cristoforo (Curate) on May 08, 2012 at 18:12 UTC
The hashes, `%proph_prots, %euk_prots, %vir_prots` are not initialized with any values. If the only parameters you are using from the file are: `$Query_id, $Subj_id, $bit_score`, you could make your initialization line as: `my ($Query_id, $Subj_id, $bit_score) = (split /\t/, $line)[0, 2, -1];` Update: Those are hash refs in the Flag() function but they are being used with regular hash notation/syntax. (You have not declared `use strict;` at the beginning of the script. Thats how I found the uninitialized hashes mentioned above.)	[reply] [d/l] [select]
Re^3: help with hash or arrays or hash references by hbm (Hermit) on May 08, 2012 at 15:17 UTC
By chance, are ALL your resulting Flags "Bact"? You are passing in hash references, but not dereferencing them; thus it seems your IFs will always fail. Seems to me you should have this: `#if (exists $proph_prots{$Subj_id}){ if (exists $$proph_prots{$Subj_id}){` [download] And so on.	[reply] [d/l]
Re^3: help with hash or arrays or hash references by Anonymous Monk on May 08, 2012 at 15:34 UTC
Here is another way to write that, less typing, fixed to dereference properly ( references quick reference ) , and filtered through `perltidy -csc -otr -opr -ce -nibc -i=4` `sub Flag { my ( $Subj_id, $proph_prots, $euk_prots, $vir_prots ) = @_; return "Proph", "Phage" if exists $$proph_prots{$Subj_id}; return "Euk", "Euk" if exists $$euk_prots{$Subj_id}; return "Vir", "Phage" if exists $$vir_prots{$Subj_id}; return "Bact", "Bact"; } ## end sub Flag` [download]	[reply] [d/l]
Re^4: help with hash or arrays or hash references by AWallBuilder (Beadle) on May 09, 2012 at 12:54 UTC
Thanks for tidying this up. I was not getting just Bact before, so I'm not sure why I didn't have to dereference? I have now changed it to $$ but there is no difference in the output. Sorry I did actually have use strict, but it is at the very beginning of the script which I didn't post.	[reply]