Changing the format of output

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

Hi, All, I would like my output in a easy to read format than they wy I have got now. I would be great to have your suggestions and pointers for this please.This is how I get my output at the moment:

Sample,Genotypes,Plex,rsids
AWQ,A,W30123,rs123
AWQ,G,W30123,rs121
AWQ,C,W30123,rs1234
AWQ,N,W30123,rs122
AWQ,T,W30123,rs1213
AWQ,NN,W30122,rs1232
AWQ,NN,W30122,rs1222
AWQ,NN,W30122,rs1223
AWQ,NN,W30122,rs12121
AWQ,NN,W30122,rs12111
AWQ,NN,W30122,rs1
AWQ,G,W30121,rs143
AWQ,C,W30121,rs13
AWQ,C,W30121,rs125
AWQ,G,W30121,rs12453
AWQ,T,W30121,rs124763
AWQ,A,W30121,rs12343
AWP,T,W30123,rs123
AWP,C,W30123,rs121
AWP,C,W30123,rs1234
AWP,N,W30123,rs122
AWP,G,W30123,rs1213
AWP,G,W30122,rs1232
AWP,N,W30122,rs1222
AWP,A,W30122,rs1223
AWP,AG,W30122,rs12121
AWP,G,W30122,rs12111
AWP,C,W30122,rs1
AWP,T,W30121,rs143
AWP,G,W30121,rs13
AWP,T,W30121,rs125
AWP,C,W30121,rs12453
AWP,G,W30121,rs124763
AWP,C,W30121,rs12343
[download]

I want them in this format Which is more readable and doesn't run for 
+too many lines.

Sample,rs123,rs121,rs1234,rs122,rs1213,rs1232,rs1222,rs1223,rs12121,rs
+12111,rs1,rs143,rs13,rs125,rs12453,rs124763,rs12343
AWQ,A,G,C,N,T,NN,NN,NN,NN,NN,NN,G,C,C,G,T,A
AWP,T,C,C,N,G,G,N,A,AG,G,C,T,G,T,C,G,C
[download]

my actual code:

use Getopt::Long;
  4 use Benchmark;
  5 use Config::Config qw(/nfs/users/nfs_a/aj6/CGP/Sequenom/perl/Seque
+nom.ini);
  6 use Database::Conn;
  7 
  8 my $conn;
  9 my $snp_list = {};
 10 my $ind_list = {};
 11 my $gen_list = {};
 12 eval {
 13 
 14  $conn = Database::Conn->new('live');
 15  $conn->addConnection(DBI->connect('dbi:Oracle:SNP.world','snp','s
+np', {RaiseError =>1 , AutoCommit=>0}),'snp');
 16 my $timestarted = Benchmark->new();
 17  my $snparray = $conn->executeArrRef('snp::Sequenom::getSnpsforPle
+x');
 18 
 19  my $indsent = $conn->executeArrRef('snp::Sequenom::getIndForPlate
+Sent');
 20 #=cut
 21  foreach my $ind( @ {$indsent} ){
 22 
 23   foreach my $snp (@ {$snparray} ){
 24 
 25     my $genotype = $conn->executeArrRef('snp::Sequenom::getGenotyp
+eCalls', $ind->[0], $snp->[0]);
 26 
 27     foreach my $geno( @ {$genotype} ){
 28       #3my $i = 1;
 29       if(defined $geno->[3]){
 30 
 31 
 32         print "$geno->[1],$geno->[3],$geno->[2],$geno->[4]\n";
 33 
 34       }#end of if loop to check the genotype defined
 35       else{
 36 
 37         print "$geno->[1],NO,$geno->[2],$geno->[4]\n"
 38 
 39       }
 40 
 41 
 42     }#end of @$genotype
 43 
 44   }#end of @$snpsent

    }#end of @$indsent
[download]

The points to note are:
1.The rsids fr each plex are unique.
2.The number of rsids in each plex may vary.
3.I get all the information from the database and it is for each sample and each snp.
Thanks every one for your help,

Comment on Changing the format of output Select or Download Code

Replies are listed 'Best First'.
Re: Changing the format of output by toolic (Bishop) on May 31, 2011 at 14:24 UTC
One way is to collect the rs things in an array (@samples) and the AW things in a hash-of-arrays inside your nested for-loops, then print it all out after the loops. UNTESTED: `my @samples; my %aws; foreach my $geno( @ {$genotype} ){ push @samples, $geno->[4]; if(defined $geno->[3]){ push @{ $aws{$geno->[1]} }, $geno->[3]; }#end of if loop to check the genotype defined else{ push @{ $aws{$geno->[1]} }, 'NO'; } }#end of @$genotype print 'Sample,'; print(join ',', @samples); print "\n"; for (keys %aws) { print "$_,"; print(join ',', @{ $aws{$_} }); print "\n"; }` [download]	[reply] [d/l]
Re: Changing the format of output by Anonymous Monk on May 31, 2011 at 23:10 UTC
my actual code: Every one of those line numbers is a syntax error	[reply]