Help for a newbie, please

jenifer

Hi.
I'm trying to collapse 2 tables in 1 as follows:
table 1

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 LOC_Os01g01020    1    -1    8174    9019    LOC_Os01g01020            CDS-ANE

R02-TIGRv4S1-000003F    2    1    33031    33967    LOC_Os02g01060    33032    33966    FL-AE

R02-TIGRv4S1-000007F    2    1    78460    79563    LOC_Os02g01140    78174    79540    FL-AE

table 2

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 AK062483    001-103-G07    R02-TIGRv4S1-000003F

K067036    J013092C19    R02-TIGRv4S1-000007F

AK0624543    prueba    R02-TIGRv4S1-000003F

outfile

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LOC_Os01g01020    1    -1    8174    9019    LOC_Os01g01020            CDS-ANE

R02-TIGRv4S1-000003F    2    1    33031    33967    LOC_Os02g01060    33032    33966    FL-AE    AK062483    001-103-G07    R02-TIGRv4S1-000003F

R02-TIGRv4S1-000003F    2    1    33031    33967    LOC_Os02g01060    33032    33966    FL-AE    AK0624543    prueba    R02-TIGRv4S1-000003F

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:

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 #! usr/bin/perl

use strict;

my $lista_1= shift or die;

my $lista_2= shift or die;

my $salida= shift or die;

open (ARCHIVO_1, "$lista_1");

open (ARCHIVO_2, "$lista_2");

open (SALIDA, ">>$salida");

my @tabla_1= <ARCHIVO_1>;

my @tabla_2= <ARCHIVO_2>;

close ARCHIVO_1;

close ARCHIVO_2;

my %hash='';

#####################################################################################

my $a= scalar @tabla_1;

my $b= scalar @tabla_2;

for (my $i=0; $i<$a ; $i++) {

    my @fila_tabla1= split ("\t", @tabla_1[$i]);

    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];

    for (my $j=0; $j<$b; $j++) {

    my @fila_tabla2= split ("\t", @tabla_2[$j]);

    my ($col_A,$col_B,$col_C)=@fila_tabla2[0,1,2];

        if ($col_1 eq $col_C) {

        print SALIDA "$tabla_1[$i]\t$tabla_2[$j]\n";

        $hash{$col_1}=1;

        $j++;

        }elsif ($j == $b-1) { 

            unless $hash{$col_1}=1{

                print SALIDA "$tabla_1[$i]\n";

            }

        }else{

        $j++;

        }

    }    

}

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)

KevinADC

The code you posted should not even compile as there is a syntax error here:

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unless $hash{$col_1}=1{

should be:

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unless ($hash{$col_1}=1) {

but using the assignment operator "=" is also wrong, you should be using a comparison operator "==":

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unless ($hash{$col_1} == 1){

So after fixing all that and I run your script I get this output:

Expand|Select|Wrap|Line Numbers

 LOC_Os01g01020    1    -1    8174    9019    LOC_Os01g01020            CDS-ANE
 
R02-TIGRv4S1-000003F    2    1    33031    33967    LOC_Os02g01060    33032    33966    FL-AE

    AK0624543    prueba    R02-TIGRv4S1-000003F

R02-TIGRv4S1-000007F    2    1    78460    79563    LOC_Os02g01140    78174    79540    FL-AE

KevinADC

See if you can figure this out, if not, ask questions:

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 #!/usr/bin/perl

use strict;

use warnings;

my $lista_1 = shift or die;

my $lista_2 = shift or die;

my $salida  = shift or die;

open (ARCHIVO_1, $lista_1);

open (ARCHIVO_2, $lista_2);

my @tabla_1 = <ARCHIVO_1>;

chomp (@tabla_1);

my @tabla_2 = <ARCHIVO_2>;

chomp (@tabla_2);

close ARCHIVO_1;

close ARCHIVO_2;

my %hash = ();

my @order = ();

#####################################################################################

my $header = shift @tabla_1;

foreach my $line (@tabla_1) {

   chomp $line;

   my ($key) = $line =~ /^(\S+)/;

   push @order, $key; 

   push @{$hash{$key}},$line;

}

foreach my $line (@tabla_2) {

   chomp $line;

   my ($key) = $line =~ /(\S+)$/;

   push @{$hash{$key}},$line;

}

open (SALIDA, ">>$salida");

print SALIDA $header,"\n";

foreach my $key (@order) {

   print SALIDA shift @{$hash{$key}},"\n";

   foreach my $line (@{$hash{$key}}) {

      print SALIDA "     $line\n";

   }

}

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:

Expand|Select|Wrap|Line Numbers

 LOC_Os01g01020    1    -1    8174    9019    LOC_Os01g01020            CDS-ANE

R02-TIGRv4S1-000003F    2    1    33031    33967    LOC_Os02g01060    33032    33966    FL-AE

     AK062483    001-103-G07    R02-TIGRv4S1-000003F

     AK0624543    prueba    R02-TIGRv4S1-000003F

R02-TIGRv4S1-000007F    2    1    78460    79563    LOC_Os02g01140    78174    79540    FL-AE

     K067036    J013092C19    R02-TIGRv4S1-000007F

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.

jenifer

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

Help for a newbie, please

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