in reply to Re^2: Memory issue with large cancer gene data structure
in thread Memory issue with large cancer gene data structure
Here is the next iteration. This now includes some code to avoid double counting of the same site of mutation for the same patient (looks very similar to your original code...). You can chose between printing the full matrix or only the relevant ones by uncommenting one of two lines close to the end of the code. Hope this is helpful.
use strict; use warnings; my %site_length_catch; my %sites; my $maxsite = 0; <DATA>; # skip header foreach (<DATA>) { chomp; # split and give meaningful names my( $gene, $patient, $diagnosis, $mut_and_sit, $length ) = split /\s ++/; # clean the site my $sit = $mut_and_sit; $sit =~ s/\D//g; # store patient to avoid double counting $site_length_catch{$gene}{$sit}{$patient} = 1; # store all sites with mutations $sites{$sit} = 1; $maxsite = $sit > $maxsite ? $sit : $maxsite; } # now remove double counted patients from the data structure foreach my $gene ( values %site_length_catch) { for my $count ( values %$gene ) { $count = keys %$count; # in scalar context you get the + number of keys } } # print table in desired format # uncomment one of the following two lines my @sitesprinted = sort { $a <=> $b } keys %sites; # sparse printing #my @sitesprinted = 1..$maxsite; # full printing # header first print "Gene"; print "\tsite $_" for @sitesprinted; print "\n"; # now the data foreach my $gene (keys %site_length_catch) { print $gene; print "\t", $site_length_catch{$gene}{$_} // 0 for @sitesprint +ed; print "\n"; } __DATA__ Gene Name Patient ID Patient Diagnosis Ammino Acid Mutation a +nd Sit Protein Length AAK1 19679 adenocarcinoma L661I 21265 AAK1 19679 adenocarcinoma L664T 21265 AAK1 19679 adenocarcinoma L664T 21265 AAK1 19679 adenocarcinoma L664T 21265 AAK1 19679 adenocarcinoma L664T 21265 AAK1 19679 adenocarcinoma L664T 21265 AAK1 19676 adenocarcinoma L664T 21265 AAK1 19677 adenocarcinoma L64F 21265 AAK1 19678 adenocarcinoma L64R 21265 FKT1 101063 ER-PR-sitive_carcinoma p.L52R 2773 FKT1 103872 ER-PR-sitive_carcinoma p.E17K 2773 FKT1 107590 ER-PR-sitive_carcinoma p.E17K 2773 FKT1 107600 ER-PR-sitive_carcinoma p.E17K 2773 FKT1 1135911 NS E17K 2773 TET3 152 chronic_lymocytic_leukaemia p.R401H 10982 TET3 587220 adenocarcinoma M935V 10982 TET3 587220 adenocarcinoma R1534Q 10982 TET3 587256 adenocarcinoma G1356R 10982 TET3 587338 adenocarcinoma G1356W 10982
As per your second table, I am optimistic that it is a relatively simple modification only.
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Re^4: Memory issue with large cancer gene data structure
by ZWcarp (Beadle) on Jul 30, 2013 at 18:36 UTC | |
Re^4: Memory issue with large cancer gene data structure
by ZWcarp (Beadle) on Aug 08, 2013 at 15:29 UTC | |
by hdb (Monsignor) on Aug 21, 2013 at 13:06 UTC | |
Re^4: Memory issue with large cancer gene data structure
by ZWcarp (Beadle) on Aug 08, 2013 at 15:30 UTC |
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