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P: 2
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Hi.
I'm trying to collapse 2 tables in 1 as follows:
table 1 - LOC_Os01g01020 1 -1 8174 9019 LOC_Os01g01020 CDS-ANE
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R02-TIGRv4S1-000003F 2 1 33031 33967 LOC_Os02g01060 33032 33966 FL-AE
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R02-TIGRv4S1-000007F 2 1 78460 79563 LOC_Os02g01140 78174 79540 FL-AE
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table 2 - AK062483 001-103-G07 R02-TIGRv4S1-000003F
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K067036 J013092C19 R02-TIGRv4S1-000007F
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AK0624543 prueba R02-TIGRv4S1-000003F
outfile -
LOC_Os01g01020 1 -1 8174 9019 LOC_Os01g01020 CDS-ANE
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R02-TIGRv4S1-000003F 2 1 33031 33967 LOC_Os02g01060 33032 33966 FL-AE AK062483 001-103-G07 R02-TIGRv4S1-000003F
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R02-TIGRv4S1-000003F 2 1 33031 33967 LOC_Os02g01060 33032 33966 FL-AE AK0624543 prueba R02-TIGRv4S1-000003F
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R02-TIGRv4S1-000007F 2 1 78460 79563 LOC_Os02g01140 78174 79540 FL-AE K067036 J013092C19 R02-TIGRv4S1-000007F
I made this, but it didn't work: - #! usr/bin/perl
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use strict;
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my $lista_1= shift or die;
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my $lista_2= shift or die;
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my $salida= shift or die;
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open (ARCHIVO_1, "$lista_1");
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open (ARCHIVO_2, "$lista_2");
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open (SALIDA, ">>$salida");
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my @tabla_1= <ARCHIVO_1>;
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my @tabla_2= <ARCHIVO_2>;
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close ARCHIVO_1;
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close ARCHIVO_2;
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my %hash='';
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#####################################################################################
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my $a= scalar @tabla_1;
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my $b= scalar @tabla_2;
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for (my $i=0; $i<$a ; $i++) {
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my @fila_tabla1= split ("\t", @tabla_1[$i]);
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my ($col_1,$col_2,$col_3,$col_4,$col_5,$col_6,$col_7,$col_8)= @fila_tabla1[0,1,2,3,4,5,6,7];
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for (my $j=0; $j<$b; $j++) {
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my @fila_tabla2= split ("\t", @tabla_2[$j]);
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my ($col_A,$col_B,$col_C)=@fila_tabla2[0,1,2];
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if ($col_1 eq $col_C) {
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print SALIDA "$tabla_1[$i]\t$tabla_2[$j]\n";
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$hash{$col_1}=1;
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$j++;
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}elsif ($j == $b-1) {
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unless $hash{$col_1}=1{
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print SALIDA "$tabla_1[$i]\n";
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}
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}else{
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$j++;
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}
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}
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}
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The problem is this: never complys whith any of the conditions ( and then, the output is empty) and I don't understand why. Help!!! Thanks. (Sorry if I wrote something wrong, english is not my native lenguage)
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| Expert 2.5K+
P: 4,059
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The code you posted should not even compile as there is a syntax error here:
should be: - unless ($hash{$col_1}=1) {
but using the assignment operator "=" is also wrong, you should be using a comparison operator "==": - unless ($hash{$col_1} == 1){
So after fixing all that and I run your script I get this output: - LOC_Os01g01020 1 -1 8174 9019 LOC_Os01g01020 CDS-ANE
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R02-TIGRv4S1-000003F 2 1 33031 33967 LOC_Os02g01060 33032 33966 FL-AE
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AK0624543 prueba R02-TIGRv4S1-000003F
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R02-TIGRv4S1-000007F 2 1 78460 79563 LOC_Os02g01140 78174 79540 FL-AE
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| Expert 2.5K+
P: 4,059
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See if you can figure this out, if not, ask questions: - #!/usr/bin/perl
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use strict;
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use warnings;
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my $lista_1 = shift or die;
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my $lista_2 = shift or die;
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my $salida = shift or die;
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open (ARCHIVO_1, $lista_1);
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open (ARCHIVO_2, $lista_2);
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my @tabla_1 = <ARCHIVO_1>;
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chomp (@tabla_1);
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my @tabla_2 = <ARCHIVO_2>;
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chomp (@tabla_2);
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close ARCHIVO_1;
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close ARCHIVO_2;
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my %hash = ();
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my @order = ();
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#####################################################################################
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my $header = shift @tabla_1;
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foreach my $line (@tabla_1) {
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chomp $line;
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my ($key) = $line =~ /^(\S+)/;
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push @order, $key;
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push @{$hash{$key}},$line;
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}
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foreach my $line (@tabla_2) {
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chomp $line;
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my ($key) = $line =~ /(\S+)$/;
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push @{$hash{$key}},$line;
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}
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open (SALIDA, ">>$salida");
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print SALIDA $header,"\n";
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foreach my $key (@order) {
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print SALIDA shift @{$hash{$key}},"\n";
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foreach my $line (@{$hash{$key}}) {
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print SALIDA " $line\n";
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}
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}
The output is not exactly like what you posted but that would be easy to change. I just went ahead and put all the lines from tabla_2 under the corresponding line in tabla_1 instead of printing the tabla_1 lines more than once: - LOC_Os01g01020 1 -1 8174 9019 LOC_Os01g01020 CDS-ANE
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R02-TIGRv4S1-000003F 2 1 33031 33967 LOC_Os02g01060 33032 33966 FL-AE
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AK062483 001-103-G07 R02-TIGRv4S1-000003F
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AK0624543 prueba R02-TIGRv4S1-000003F
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R02-TIGRv4S1-000007F 2 1 78460 79563 LOC_Os02g01140 78174 79540 FL-AE
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K067036 J013092C19 R02-TIGRv4S1-000007F
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The code could probably be written a bit better but will leave that up to you or anyone else if they wish to contribute further.
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P: 2
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Well, first of all, thanks for your help. I've never expected an answer so fast.
Second, this is very usefull because I've never worked with the push function (well, I started to "program" 4 months ago...yes, really, really newbie, so this world is new for me).
First I have to read about this and after I'm going to start to do questions.
So, ones more, thanks
| | | |  Question stats - viewed: 1086
- replies: 3
- date asked: Jul 2 '08
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