diff scripts/sorting.pl @ 22:7997c93ee479

last attempt to install perl as part of linkyx

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/sorting.pl	Thu Sep 11 19:40:01 2014 -0400
@@ -0,0 +1,38 @@
+#!/usr/bin/perl -w
+use strict;
+#usage: perl sorting.pl A/
+
+my @inputs = @ARGV;
+chomp(@inputs);
+
+my $dir = $inputs[0];
+my $reference = $inputs[1];
+my $LINKYX_PATH = $inputs[2];
+my $results = "X_results.txt"; 
+my %hash = (); #contig <-> family member with the maximal number of not uniquely mapped reads
+my $contig; my $count=0; my $iso;
+
+open(RESULTS_FILE, $results) or die "(sorting.pl) Impossible to open source file: $!\n";
+
+	while (<RESULTS_FILE>) { 
+		$contig = $_; chomp($contig);
+		$count = `bash $LINKYX_PATH/scripts/number_of_not_uniq_mapped_reads.sh $dir $contig`;
+		$hash{$contig} = $count; 
+	}
+
+foreach (sort {$hash{$a} <=> $hash{$b}} keys %hash) {
+	  print "$_ $hash{$_}";
+
+			#get sequence
+			print "% of not uniquely mapped reads for contig ".$_.": ".$hash{$_}."\n";
+			system("perl $LINKYX_PATH/scripts/get_sequences_based_on_ids.pl $reference $_");
+
+			$iso = `bash $LINKYX_PATH/scripts/isoform_exists.sh $_ references/reference_contig_names`;
+			if ($iso eq '') {
+ 				print "No isoforms.\n";
+			} else {
+				print "Isoforms exists:\n";
+				print $iso;
+			}
+			print "----------\n";
+	}
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