From 6fb713e0939231ed8618602a0020a9914ed75bcc Mon Sep 17 00:00:00 2001
From: "Teresita M. Porter" <terrimporter@gmail.com>
Date: Thu, 4 Feb 2021 22:01:38 -0500
Subject: [PATCH] Delete qiime_unite_to_rdp.plx

---
 qiime_unite_to_rdp.plx | 237 -----------------------------------------
 1 file changed, 237 deletions(-)
 delete mode 100644 qiime_unite_to_rdp.plx

diff --git a/qiime_unite_to_rdp.plx b/qiime_unite_to_rdp.plx
deleted file mode 100644
index c125a92..0000000
--- a/qiime_unite_to_rdp.plx
+++ /dev/null
@@ -1,237 +0,0 @@
-#!/usr/bin/perl
-# Teresita M. Porter, Feb. 2/21
-# Script to convert UNITE QIIME-formatted files to re-train the stand-alone RDP classifier v2.13
-# USAGE perl qiime_unite_to_rdp.plx file.fasta file.taxonomy
-
-use strict;
-use warnings;
-use Data::Dumper;
-
-# declare vars
-my $i=0;
-my $line;
-my $sh;
-my $lineage;
-my $j;
-my $seq;
-my $index=0;
-my $taxonname;
-my $previousindex;
-my $rankindex;
-my $rankname;
-my $taxon;
-my $rankletter;
-my $tmp;
-my $previoustaxon;
-my $newlineage;
-my $k=0;
-
-# declare arrays
-my @fasta;
-my @tax;
-my @line;
-my @lineage;
-my @taxon;
-
-# declare hashes
-my %tax; #id = sh, val = qiime formatted lineage
-my %taxon; #id = k__taxon; val = taxonindex
-my %rankname; #id = letter; val = rankname
-my %rankindex; # id = letter; val = rankindex
-my %problems; # id = taxon g__genus; val = 1
-
-# create rankname hash
-%rankname = ('k', "kingdom",
-		'p', "phylum",
-		'c', "class",
-		'o', "order",
-		'f', "family",
-		'g', "genus",
-		's', "species");
-
-# create rankindex hash
-%rankindex = ('k', 1,
-		'p', 2,
-		'c', 3,
-		'o', 4,
-		'f', 5,
-		'g', 6,
-		's', 7);
-
-# create problems hash
-# contains non-unique taxa (ex. same genus name found in two different families)
-%problems = ('g__Cryptococcus','1',
-		'g__Cenangiopsis','1',
-		'g__Aleurina','1',
-		'g__Cylindrium','1',
-		'g__Brevicollum','1');
-
-open (FASTA, "<", $ARGV[0]) || die "Error can't open fasta file: $!\n";
-@fasta = <FASTA>;
-close FASTA;
-
-open (TAX, "<", $ARGV[1]) || die "Error can't open taxonomy file: $!\n";
-@tax = <TAX>;
-close TAX;
-
-# first parse id -> lineage taxonomy file
-while ($tax[$i]) {
-	$line = $tax[$i];
-	chomp $line;
-
-	@line = split(' ',$line);
-	$sh = $line[0];
-	$lineage = $line[1];
-
-	$tax{$sh} = $lineage;
-
-	$i++;
-}
-$i=0;
-
-# create reformatted outfile
-open (OUT, ">>", "mytrainseq.fasta") || die "Error can't open outfile: $!\n";
-
-# first reformat fasta file for training rdp classifier
-while ($fasta[$i]) {
-	$line = $fasta[$i];
-	chomp $line;
-
-	if ($line =~ /^>/) { #header
-		$sh = $line;
-		$sh =~ s/^>//g;
-
-		if (exists $tax{$sh}) {
-			$lineage = $tax{$sh};
-
-			# parse through lineage to handle unidentified
-			@lineage = split(/;/, $lineage);
-			
-			while ($lineage[$k]) {
-				$taxon = $lineage[$k];
-
-				# handle unidentified
-				if ($taxon =~ /unidentified/) {
-					$taxon = $previoustaxon."_".$taxon; # append previous taxon as prefix
-					$lineage[$k] = $taxon;
-					$previoustaxon = $taxon; # only needed if next taxon is unidentified
-				}
-
-				# handle non-unique taxa (taxa of the same name found in more than one higher-level group, ex. same genus name in two different families)
-				if (exists $problems{$taxon}) {
-					$taxon = $previoustaxon."_".$taxon; #append previous taxon as prefix
-					$lineage[$k] = $taxon;
-					$previoustaxon = $taxon; # only needed if next taxon is unidentified
-				}
-				
-				else {
-					$previoustaxon = $taxon; #only needed if next taxon is unidentified
-				}
-
-				$k++;
-			}
-			$k=0;
-
-			$newlineage = join ';', @lineage;
-		
-			print OUT ">$sh\tRoot;$newlineage;$sh\n";
-			$newlineage = "";
-			$j = $i+1;
-			$seq = $fasta[$j];
-			chomp $seq;
-			print OUT $seq."\n";
-		}
-		else {
-			print "Couldn't find SH $sh in hash\n";
-		}
-	}
-	$i++;
-}
-$i=0;
-close OUT;
-
-# create newly formatted taxonomy file
-open (OUT2, ">>", "mytaxon.txt") || die "Can't open taxonomy outfile: $!\n";
-
-# print out taxonomy file for classifier
-while ($tax[$i]) {
-	$line = $tax[$i];
-	chomp $line;
-
-	# add root
-	if ($i==0) {
-		$index=0;
-		$taxonname = "Root";
-		$previousindex = "-1";
-		$rankindex = "0";
-		$rankname = "rootrank";
-		print OUT2 $index."*".$taxonname."*".$previousindex."*".$rankindex."*".$rankname."\n";
-		$taxon{$taxonname} = $index;
-		$previousindex = $index;
-		$index++;
-	}
-
-	# add lineage (kingdom to species)
-	@line = split(' ', $line);
-	$sh = $line[0];
-	$lineage = $line[1];
-	@lineage = split(/;/,$lineage);
-
-	foreach $taxon (@lineage) {
-
-		@taxon = split(/__/,$taxon);
-		$rankletter = $taxon[0];
-
-		if (exists $rankname{$rankletter} ) {
-			$rankname = $rankname{$rankletter};
-
-			if (exists $rankindex{$rankletter}) {
-				$rankindex = $rankindex{$rankletter};
-
-				# handle unidentified ranks
-				if ($taxon =~ /unidentified/) {
-					$taxon = $previoustaxon."_".$taxon; #append previous taxon as prefix
-					$previoustaxon = $taxon; # only needed if next taxon is unidentified
-				}
-
-				# handle non-unique taxa (ex. same genus name in two different families)
-				if (exists $problems{$taxon}) {
-					$taxon = $previoustaxon."_".$taxon; #append previous taxon as prefix
-					$previoustaxon = $taxon; # only needed if next taxon is unidentified
-				}
-
-				if (exists $taxon{$taxon} ) {
-					$tmp = $taxon{$taxon}; 
-					$previousindex = $tmp;
-					$previoustaxon = $taxon; #only needed if next taxon is unidentified
-
-				}
-				else {
-					print OUT2 $index."*".$taxon."*".$previousindex."*".$rankindex."*".$rankname."\n";
-					$taxon{$taxon} = $index;
-					$previousindex = $index;
-					$index++;
-					$previoustaxon = $taxon; #only needed if next taxon is unidentified
-
-				}
-
-			}
-			else {
-				print "Can't find rankletter $rankletter in rankindex hash\n";
-			}
-		}
-		else {
-			print "Can't find rankletter $rankletter in rankname hash\n";
-		}
-	
-	}
-
-	# add SH
-	print OUT2 $index."*".$sh."*".$previousindex."*8*SH\n";
-	$index++;
-
-	$i++;
-
-}
-$i=0;
-close OUT2;