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silva_to_rdp.pl
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silva_to_rdp.pl
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#!/usr/bin/env perl
###############################################################################
#
# silva_to_rdp.pl
#
# 1) Download the newest release of the silva database in fasta format e.g. "SSURef_NR99_115_tax_silva_trunc.fasta".
# 2) Cluster the silva database at the desired level using usearch:
# A) ./usearch7.0.1090 -sortbylength SSURef_NR99_115_tax_silva_trunc.fasta -output sorted.fa -minseqlength 1000 -notrunclabels
# B) ./usearch7.0.1090 -cluster_smallmem sorted.fa -id 0.97 -centroids nr.fasta -notrunclabels
# 3) Supply the clustered file:
# silva_to_rdp.pl -i nr.fasta
# 4) Outputs:
# A) tax.txt: A taxonomy file with 6 (genus) or 7 ranks (species). If the input sequence has less than 7 ranks a blank assignment is added (e.g. g__). If >7 ranks the first 7 are reported (the case for many eukaryotes).
# B) ref.fasta: A fasta file with the sequences, but with only the identifier in the header.
#
# Copyright (C) 2014 Mads Albertsen
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
###############################################################################
#pragmas
use strict;
use warnings;
#core Perl modules
use Getopt::Long;
#locally-written modules
BEGIN {
select(STDERR);
$| = 1;
select(STDOUT);
$| = 1;
}
# get input params
my $global_options = checkParams();
my $infa;
my $outtax;
my $outref;
my $genus;
my $Eukaryota;
$infa = &overrideDefault("infa.fa",'infa');
$outtax = &overrideDefault("tax.txt",'outtax');
$outref = &overrideDefault("ref.fasta",'outref');
$genus = &overrideDefault(0,'genus');
$Eukaryota = &overrideDefault(0,'Eukaryota');
my %tax;
my $print = 0;
my $seq = "";
my $count = 0;
my $header = "";
my $euk = "";
my $taxstring = "";
my $dub = "";
######################################################################
# CODE HERE
######################################################################
open(IN_fa, $infa) or die("Cannot read file: $infa\n");
open(OUT_tax, ">$outtax") or die("Cannot create file: $outtax\n");
open(OUT_ref, ">$outref") or die("Cannot create file: $outref\n");
while ( my $line = <IN_fa> ) {
chomp $line;
#$line =~ s/\r\n//g; # Windows handle to unix file endings
#$line =~ s/\r//g; # Windows handle to unix file endings
$count++;
if ($line =~ m/>/){
$line =~ s/>//;
$line =~ s/\*//g;
my @split = split(/ /, $line, 2);
my @splittax = split(/;/, $split[1]);
my @splitid = split(/\./, $line, 2);
my $id = "";
if (!exists($tax{$splitid[0]})){ $tax{$splitid[0]} = 1 } else { $tax{$splitid[0]}++;print "Error, discarding sequence! $splitid[0] seen $tax{$splitid[0]} times\n"; } # Check that the entry is not duplicated!
if (exists($splittax[0])) {$id = $id . "k__" . $splittax[0]} else{$id = $id . "\tk__"}
if (exists($splittax[1])) {$id = $id . ";p__" . $splittax[1]} else{$id = $id . ";p__"}
if (exists($splittax[2])) {$id = $id . ";c__" . $splittax[2]} else{$id = $id . ";c__"}
if (exists($splittax[3])) {$id = $id . ";o__" . $splittax[3]} else{$id = $id . ";o__"}
if (exists($splittax[4])) {$id = $id . ";f__" . $splittax[4]} else{$id = $id . ";f__"}
if (exists($splittax[5])) {$id = $id . ";g__" . $splittax[5]} else{$id = $id . ";g__"}
if ($genus == 0){ if (exists($splittax[6])) {$id = $id . ";s__" . $splittax[6]} else{$id = $id . ";s__"}}
if ($count > 1){
$seq = uc($seq);
$seq =~ s/U/T/g;
if ($dub == 1){ $print = 1 }
if ($euk =~ m/Eukaryota/ and $Eukaryota == 1) { $print = 0 }
if ($print == 1){
print OUT_ref "$header\n";
print OUT_ref "$seq\n";
print OUT_tax "$taxstring\n";
}
$print = 0;
$seq = "";
$header = "";
$taxstring = "";
$euk = "";
$dub = "";
}
$header = ">$splitid[0]";
$taxstring = "$splitid[0]\t$id";
$euk = $splittax[0];
$dub = $tax{$splitid[0]};
} else {
$seq = $seq . $line;
}
}
$seq = uc($seq);
$seq =~ s/U/T/g;
if ($dub == 1){$print = 1}
if ($euk =~ m/Eukaryota/ and $Eukaryota == 1) { $print = 0 }
if ($print == 1){
print OUT_ref "$header\n";
print OUT_ref "$seq\n";
print OUT_tax "$taxstring\n";
}
close IN_fa;
close OUT_ref;
######################################################################
# TEMPLATE SUBS
######################################################################
sub checkParams {
#-----
# Do any and all options checking here...
#
my @standard_options = ( "help|h+", "infa|i:s", "outtax|t:s", "outref|r:s", "genus|g:+", "Eukaryota|e:+");
my %options;
# Add any other command line options, and the code to handle them
#
GetOptions( \%options, @standard_options );
#if no arguments supplied print the usage and exit
#
exec("pod2usage $0") if (0 == (keys (%options) ));
# If the -help option is set, print the usage and exit
#
exec("pod2usage $0") if $options{'help'};
# Compulsosy items
#if(!exists $options{'infile'} ) { print "**ERROR: $0 : \n"; exec("pod2usage $0"); }
return \%options;
}
sub overrideDefault
{
#-----
# Set and override default values for parameters
#
my ($default_value, $option_name) = @_;
if(exists $global_options->{$option_name})
{
return $global_options->{$option_name};
}
return $default_value;
}
__DATA__
=head1 NAME
silva_to_rdp.pl
=head1 COPYRIGHT
copyright (C) 2014 Mads Albertsen
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
=head1 DESCRIPTION
=head1 SYNOPSIS
silva_to_rdp.pl -i [-h -t -r -g]
[-help -h] Displays this basic usage information
[-infa -i] Usearch clustered fasta file of the original silva file
[-outtax -t] Output taxonomic file for the rdp classifier
[-outref -r] Output reference sequences for the rdp classifier
[-genus -g] Report genus level assignments instead of species (flag, default no)
[-Eukaryota -e] Flag to indicate that Eukaryota should be removed.
=cut