Re: Re: Unique Variable names...

My input data file would look something like:

AFFX-BioB-5_at    20    20    200.2    P    0.001
AFFX-BioB-M_at    20    20    400.4    P    0.002 
AFFX-BioB-3_at    20    20    200.5    P    0.003
[download]

I want the 4th column, with the signal data. Actually, that other subroutine gets only the first column from the first file. I didn't know how to do that otherwise, since everything else was in a loop. This way, I have everything set to look like (if it worked anyway):

AFFX-BioB-5_at    200.0   300.0   400.0
AFFX-BioB-M_at    200.0   300.0   400.0
AFFX-BioB-3_at  200.0   300.0   400.0
[download]

Thanks for your suggestions!!
Bioinformatics

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Re: Re: Re: Unique Variable names... by CountZero (Bishop) on Jul 30, 2003 at 19:48 UTC
OK, now we're talking. Assuming you want a result which is first the AFFX-BioB-xxx_at-identifier, followed by all signal-data which are connected to this identifier, I suggest: you drop the `get_targets` sub and all references to it. Then you change your sub get_signal to: `while (@filename) { my $i; $file=shift @filename; use Cwd 'chdir'; chdir "./data"; open (FILE, "$file") or die; while (<FILE>) { next while $i++ <= 14; (my $id, undef, undef, my $signal, undef, undef)=split(/\t +/); push @{$outputdata{$id}}, $signal; } close (FILE); }` [download] After having run this sub over all your files you will find in %outputdata a nicely ordered (per identifier) structure of your signal-data. "Printing this datastructure goes as follows: `for $id (keys %outputdata) { print "$id:\t",(join("\t",@{$outputdata{$id}})),"\n"; }` [download] Of course you can print it to a filehandle. This is a format which is suitable to be imported in a database or a spreadsheet. The "magic" of using references to anonymous arrays may perhaps be a bit too deep for someone who is just starting to program, but if you read Chapters 8 and 9 of the Camel book a few times and study the examples given, much will become clearer. CountZero "If you have four groups working on a compiler, you'll get a 4-pass compiler." - Conway's Law	[reply] [d/l] [select]

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Re: Re: Re: Unique Variable names...
by CountZero (Bishop) on Jul 30, 2003 at 19:48 UTC

OK, now we're talking.

Assuming you want a result which is first the AFFX-BioB-xxx_at-identifier, followed by all signal-data which are connected to this identifier, I suggest:

you drop the get_targets sub and all references to it.

Then you change your sub get_signal to:

    while (@filename) {
        my $i;
        $file=shift @filename;
        use Cwd 'chdir';
        chdir "./data";
        open (FILE, "$file") or die;
        while (<FILE>) {
            next while $i++ <= 14;
            (my $id, undef, undef, my $signal, undef, undef)=split(/\t
+/);
        push @{$outputdata{$id}}, $signal;
        }
        close (FILE);
    }
[download]

After having run this sub over all your files you will find in %outputdata a nicely ordered (per identifier) structure of your signal-data.

"Printing this datastructure goes as follows:
```
for $id (keys %outputdata) {
    print "$id:\t",(join("\t",@{$outputdata{$id}})),"\n";
}
[download]
```
Of course you can print it to a filehandle. This is a format which is suitable to be imported in a database or a spreadsheet.

CountZero

"If you have four groups working on a compiler, you'll get a 4-pass compiler." - Conway's Law

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