problem with loop

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

Dear all, I am trying to write a fairly simple script that takes a pathway, and writes out all the possible pairs and the 'steps' between the pairs, ie. 1 means that they are beside each other in the pathway and 2 means that there is another unit between them. However my output for the 'steps' is incorrect, the second time I go through everything is +1 (compare desired and current output). Any help is appreciated. thanks.

input

PA5098  PA5100  PA5092  PA3175
[download]

desired output

PA5098  PA5100  1
PA5098  PA5092  2
PA5098  PA3175  3
PA5100  PA5092  1
PA5100  PA3175  2
PA5092  PA3175  1
[download]

current output

PA5098     PA5100    1
PA5098     PA5092    2
PA5098     PA3175    3
PA5100     PA5092    2
PA5100     PA3175    3
PA5092     PA3175 3
[download]

code

############# open pathways output list with PA01 locus IDs
my $in=$ARGV[1] || "pathways.col";
open (IN,$in) or die "cannot open $in\n";
##
my $out="$in.$org.stepSize.tab";
open(OUT,">",$out);
#
my %HoCplx2ID; my %HoPwyPair;my %HoPairs;
while (my $lines=<IN>){
        next if ($lines =~/^#/);
        next if ($lines =~/^UNIQUE-ID/);
        chomp $lines;
        my @cols=split(/\t/,$lines);
        my $cmplxID=$cols[0];
        my $cmplxNm=$cols[1];
        my @restCols=@cols[2..$#cols];
        my @cycIDs=grep(/^GCXG-/, @restCols);
        @cycIDs=grep($_ ne '',@cycIDs);
        my $pwySize=scalar(@cycIDs);
        push (@{$HoCplx2ID{$cmplxID}},@cycIDs);
}
close(IN);
###########
my %HoP;
foreach my $pwy (keys %HoCplx2ID){
        my @genes=@{$HoCplx2ID{$pwy}};
        my $numbGenes=scalar(@genes);
                for (my $i=0;$i<$numbGenes;$i++){
                for (my $j=1;$j<$numbGenes;$j++){
                                                         my $pair=join
+("-",$HoCycID2Loc{$genes[$i]},$HoCycID2Loc{$genes[$j]});
                        my $rev_pair=join("-",$HoCycID2Loc{$genes[$j]}
+,$HoCycID2Loc{$genes[$i]});
                        if (($genes[$i] ne $genes[$j]) && (!exists($Ho
+P{$rev_pair}))){
                                print OUT join("\t",$HoCycID2Loc{$gene
+s[$i]},$HoCycID2Loc{$genes[$i+1]},$j)."\n";
                                $HoP{$pair}=1;
                }
        }
        }
        }
[download]

Comment on problem with loop Select or Download Code

Replies are listed 'Best First'.
Re: problem with loop by McA (Priest) on Oct 27, 2014 at 11:50 UTC
Hi, probably something like this: `#!/usr/bin/perl use strict; use warnings; use 5.010; my @list = qw(PA5098 PA5100 PA5092 PA3175); for (my $i = 0; $i < @list - 1; $i++) { for (my $j = $i + 1; $j < @list; $j++) { my $diff = $j - $i; print "$list[$i] $list[$j] $diff\n"; } }` [download] Be aware: You need a special case when list has less than two elements. Regards McA	[reply] [d/l]
Re^2: problem with loop by AnomalousMonk (Archbishop) on Oct 27, 2014 at 13:51 UTC
You need a special case when list has less than two elements. No special case seems needed: inner loop just executes 0 times. (Update: Also works with 5.8.9.)	[reply]
Re^2: problem with loop by Anonymous Monk on Oct 27, 2014 at 11:53 UTC
thanks - simple	[reply]
Re: problem with loop by AnomalousMonk (Archbishop) on Oct 27, 2014 at 13:43 UTC
Another way. No special-casing needed for 0, 1 element arrays/lists. `c:\@Work\Perl>perl -wMstrict -le "my @node_names = qw(PA5098 PA5100 PA5092 PA3175); ;; for my $i (0 .. $#node_names) { my @following = $i+1 .. $#node_names; for my $j (@following) { print qq{$node_names[$i] $node_names[$j] }, $j - $i; } } " PA5098 PA5100 1 PA5098 PA5092 2 PA5098 PA3175 3 PA5100 PA5092 1 PA5100 PA3175 2 PA5092 PA3175 1` [download]	[reply] [d/l]
Re: problem with loop by 2teez (Vicar) on Oct 27, 2014 at 14:51 UTC
Or this: `use warnings; use strict; my @p = qw[PA5098 PA5100 PA5092 PA3175]; for my $i ( 0 .. $#p ) { last if $i == $#p; for my $j ( 0 .. $#p ) { print join( " " => ( $p[$i], $p[$j], $j - $i ) ), $/ unless $i + >= $j; } }` [download] Output `PA5098 PA5100 1 PA5098 PA5092 2 PA5098 PA3175 3 PA5100 PA5092 1 PA5100 PA3175 2 PA5092 PA3175 1` [download] I kind of like AnomalousMonk solution, because it has no help from ifs and unless. McA solution is also cool for me, but I don't like C-for loop in perl! :) If you tell me, I'll forget. If you show me, I'll remember. if you involve me, I'll understand. --- Author unknown to me	[reply] [d/l] [select]