Beefy Boxes and Bandwidth Generously Provided by pair Networks
XP is just a number

Re^3: Memory issue with cancer data (analogy)

by BrowserUk (Pope)
on Jul 26, 2013 at 01:28 UTC ( #1046441=note: print w/replies, xml ) Need Help??

in reply to Re^2: Memory issue with cancer data (analogy)
in thread Memory issue with cancer data (analogy)

See how you get on with this:

#! perl -sw use strict; <>; #discard header line my %table; my %lengths; while( <> ) { my( $gene, $id, undef, $site, $len ) = split; my( $pos ) = $site =~ m[(\d+)]; ## extract the digits from t +he site undef $table{ $gene }{ $pos }{ $id }; ## adds the id as a key with + no value (saves space!) $lengths{ $gene } = $len; ## Save the gene lengths for + later } #print 'output header line here if required'; for my $gene ( sort keys %table ) { print "$gene"; my $p = 1; for my $pos ( sort{ $a <=> $b } keys %{ $table{ $gene } } ) { print "\t0" x ( $pos - $p ), "\t", scalar keys %{ $table{ $gen +e }{ $pos } }; $p = $pos + 1; } print "\t0" x ( $lengths{ $gene } - $p ), "\n"; }

Invoke it as < theInputFile > theOutputFile. It shouldn't take more than a minute or two to run.

It'll probably need tweaking. Like adding an appropriate header line if that is a requirement. I couldn't work out what would be needed as all the output lines will be different lengths, as the genes are different lengths.

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

Log In?

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://1046441]
and all is quiet...

How do I use this? | Other CB clients
Other Users?
Others romping around the Monastery: (5)
As of 2018-03-25 01:49 GMT
Find Nodes?
    Voting Booth?
    When I think of a mole I think of:

    Results (299 votes). Check out past polls.