diff phyloconversion/remove_phytab_dupes.pl @ 0:5b9a38ec4a39 draft default tip

First commit of old repositories

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloconversion/remove_phytab_dupes.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,60 @@
+#!/usr/bin/perl
+use strict;
+
+
+
+my $infile=$ARGV[0];
+my $keeplongest=$ARGV[1];
+my $ignoregaps=$ARGV[2];
+my $uniout=$ARGV[3];
+my $dupout=$ARGV[4];
+
+open IN, $infile or die "Cannot open $infile\n";
+
+my %UniquesHash;
+my @DupeArray;
+
+while(<IN>){
+	my $row = $_;
+	chomp($row);
+	my @column = split(/\t/, $row);
+	my $species = $column[0];
+	my $partition = $column[1];
+	my $id = $column[2];
+	my $sequence = $column[3];
+
+	if(exists $UniquesHash{$species}{$partition}){
+		my @dupeseq = split(/\t/, $UniquesHash{$species}{$partition});
+		my ($savlen,$curlen);
+		if($ignoregaps==1){
+			my $nogapsav = $dupeseq[1];
+			my $nogapcur = $sequence;
+			$nogapsav =~ s/\-//g;
+			$nogapcur =~ s/\-//g;
+			$savlen = length($nogapsav);
+			$curlen = length($nogapcur);
+		}else{
+			$savlen = length($dupeseq[1]);
+			$curlen = length($sequence);
+		}
+		if($curlen > $savlen && $keeplongest==1) { 		#current is longer so keep that one
+			my $oldline = $species."\t".$partition."\t".$UniquesHash{$species}{$partition}."\n";
+			$UniquesHash{$species}{$partition} = "$id\t$sequence";
+			push(@DupeArray, $oldline);
+		}else{ 
+			push(@DupeArray, "$species\t$partition\t$id\t$sequence\n");
+		}
+	}else{
+		$UniquesHash{$species}{$partition} = "$id\t$sequence";
+	}
+}
+
+open OUT, ">".$uniout or die "Cannot open $uniout\n";
+open DUPES, ">".$dupout or die "Cannot open $dupout\n";
+
+print DUPES @DupeArray;
+for my $spname ( keys %UniquesHash ) {
+    for my $partname ( keys %{ $UniquesHash{$spname} } ) {
+         print OUT "$spname\t$partname\t$UniquesHash{$spname}{$partname}\n";
+    }
+}