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PopGenTools_3.00.pl
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#!/usr/bin/perl
#Dependencies: ANGSD (http://popgen.dk/wiki/index.php/ANGSD); ngsTools (https://github.com/mfumagalli/ngsTools); Your brain.
#ngsCovar, ngsFst, angsd, emOptim2, and sfstools in path.
## Author: Ke Bi ([email protected])
## Computational Genomics Resource Laboratory
## California Institute for Quantitative Biosciences
## University of California, Berkeley
## 238 Koshland Hall
## Berkeley, CA 94720-3102
use strict;
use warnings;
use Getopt::Std;
use Getopt::Long;
use File::Basename;
use Math::Trig;
#use Geo::Proj4;
use List::Util qw[min max];
#use Statistics::R;
&main;
exit;
sub main {
&usage if (@ARGV<1);
my $command = shift(@ARGV);
my %p = (Structure=>\&Structure, PCA=>\&PCA, ANGSD=>\&ANGSD, Adegenet=>\&Adegenet, Admixture=>\&Admixture, SNPID=>\&SNPID, SNP2D=>\&SNP2D, MERGE=>\&MERGE, SPA=>\&SPA, FST=>\&FST, Outgroup=>\&Outgroup, TREEMIX=>\&TREEMIX, DADI=>\&DADI, GEODIST=>\&GEODIST, BAYENV=>\&BAYENV, Geneland=>\&Geneland, GENEPOP=>\&GENEPOP, VCF2NEXUS=>\&VCF2NEXUS, VCF2smartPCA=>\&VCF2smartPCA,VCF2structure=>\&VCF2structure,VCF2admixture=>\&VCF2admixture,VCF2splittree=>\&VCF2splittree, VCF2SPA=>\&VCF2SPA, POPFilter=>\&POPFilter,NEXUS=>\&NEXUS,PLINK=>\&PLINK, CONTIG=>\&CONTIG, PHASE=>\&PHASE,Dxy=>\&Dxy, raxml=>\&raxml );
die("Unknown command \"$command\"\n") if (!defined($p{$command}));
&{$p{$command}};
}
sub usage {
die(qq/
Usage: PopGenTools3.00.pl <command> [<arguments>]\n
Command:
ANGSD: SNP calling, genotype calling and allel frequency
estimating using ANGSD, with or without an outgroup reference
PCA: Use ngsCovar to generate genetic covariance matrix
from genotype output by ANGSD -doGeno 32
FST: Calculate Fst using ngsFST
NEXUS: Convert genotypes (ANGSD -doGeno 2) to nexus format
GENEPOP: Convert genotypes (ANGSD -doGeno 4) to GENEPOP input
Structure: Convert genotypes (ANGSD -doGeno 4) to STRUCTURE input
Adegenet: Convert genotypes (ANGSD -doGeno 2) to adegenet input to calculate genetic distance
Admixture: Convert genotypes (ANGSD -doGeno 2) to ADMIXTURE input
SPA: Covert genotypes (ANGSD -doGeno 2) to SPA input
TREEMIX: Covert genotypes (ANGSD -doGeno 2) to Treemix input
POPFilter: Perform filtering on missing data for each sub population, require (ANGSD -doGeno 2)
PINK: prune SNPs for LD
SNPID: Identify SNP ID based on *.prob (ANGSD sfstools) and *.sfs.pos (ANGSD angsd)
SNP2D: Identify specific SNPs from 2dSFS based on *.prob (ANGSD sfstools) and *.sfs.pos (ANGSD angsd)
MERGE: merge .pos files to generate concensus .keep file for second round ANGSD
GEODIST: convert geographic coordinates to geographic distances
Geneland: Covert genotypes (ANGSD -doGeno 2) to Geneland input and covert lat and long to UTM
BAYENV: Covert genotypes (ANGSD -doGeno 2) to BAYENV input file
CONTIG: reconstruct sequence alignment based on SNPs
PHASE: convert genotype (-doGeno 2) to PHASE input file and perform PHASE analyses
Dxy: calculate Dxy using ANGSD genotype (-doGeno 2)
Outgroup: parse VCF file and make outgroup fasta
VCF2NEXUS: call SNPs from vcf then convert it to nexus format for Beauti and SNAPP
VCF2smartPCA: call SNPs from vcf then generate input files for smartPCA
VCF2structure: call SNPs from vcf then generate input files for STRUCTURE
VCF2admixture: call SNPs from vcf then generate input files for admixture
VCF2splittree: call SNPs from vcf then generate input files for splitree
VCF2SPA: call SNPs from vcf then generate input files for SPA
raxml: generating raxml input files from the alignment (bams)
\n/);
}
####################################################################################################################################################
sub Outgroup {
die(qq/
Usage PopGenomics.pl Outgroup [options]
Options: -v FILE VCF: generated by outgroup reads mapped to ingroup fasta sequences; i.e. samtools mpileup -D -S -I -B -f ingroup.fa bam1 bam2 bam3... | bcftools view - cg-> raw.vcf
-f FILE re-constructed fasta file by vcfutils.pl vcf2fq in SamTools i.e. mpileup -uf ref.fa -l filtered.bed aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq; Note "filtered.bed" is generated by using SNPcleaner.pl by Tyler Linderoth.
-c FILE original in-group reference used to align reads from outgroup libraires.
-o FILE outfile name
\n/) if (!@ARGV);
my %opts = (v=>undef, f=>undef, c=>undef, o=>undef);
getopts('v:f:c:o:', \%opts);
my $VCF = $opts{v} or die ("\nError! You must provide the name of VCF file!\n\n") ;
my $raw_ref = $opts{f} or die ("\nError! Cannot open the re-constructed fasta file!\n\n");
my $outfile = $opts{o} or die ("\nError! You must define the name of outfile!\n\n") ;
my $orig_ref = $opts{c} or die ("\nError! Original in-group reference used to align reads from outgroup libraires is not provided! \n\n") ;
my $file;
open($file, $raw_ref);
my %sequence_data;
my $new_raw_ref = 'new_raw.fa';
open (OUT, '>', $new_raw_ref);
my $start0 = time;
while (read_fasta($file, \%sequence_data)) {
print OUT ">$sequence_data{header}\n$sequence_data{seq}\n";
}
close OUT;
my $time0 = int(time - $start0);
print "Re-formatted fasta sequences $time0 sec!\n";
my $start1 = time;
my $fixed = 'new_raw_fixed.fa';
mask($new_raw_ref, $VCF, $fixed);
final($fixed, $orig_ref, $outfile);
my $time1 = int(time - $start1);
print "Made outgroup reference $time1 sec! Hew! It has taken so long!\n";
sub read_fasta {
my ($file,$seqio) = @_;
$seqio->{seq} = undef;
$seqio->{header} = $seqio->{next_header} if $seqio->{next_header};
my $file_not_empty = 0;
while (<$file>) {
$file_not_empty = 1;
next if /^\s*$/;
chomp;
if (/^>/) {
my $header = $_;
$header =~ s/^>//;
if ($seqio->{header}) {
$seqio->{next_header} = $header;
return $seqio;
}
else {
$seqio->{header} = $header;
}
}
else {
s/\s+//;
$seqio->{seq} .= $_;
}
}
if ($file_not_empty) {
return $seqio;
}
else {
$seqio->{header} = $seqio->{seq} = $seqio->{next_header} = undef;
return;
}
}
sub mask{
my ($new_raw_ref, $VCF, $fixed) = @_;
open (IN1, '<', $new_raw_ref);
open (IN2, '<', $VCF);
open (OUT, '>', $fixed);
my %data;
while (<IN1>) {
chomp (my $line = $_);
if ($line =~ m /^>/ ) {
chomp($data{$line} = <IN1>);
}
}
close IN1;
while (<IN2>) {
chomp (my @line = split /\t/, $_);
if ($line[0] =~ m/^Contig/) {
my $alt = $line[4];
my $pos = $line[1];
my $contig = '>'. $line[0];
my @alt = split /,/, $alt;
if (scalar (@alt) > 1 ) {
if ( length($data{$contig})) {
if ( length($data{$contig}) >= $pos) {
substr ($data{$contig}, $pos-1, 1) ='B';
}
}
}
}
}
close IN;
my %newdata;
foreach (keys(%data)) {
$data{$_} =~ s/[a|c|g|t|n|y|s|k|r|w|m|B|Y|S|R|K|W|M]/N/g ;
$newdata {substr($_, 7)} = $data{$_};
}
for my $key (sort {$a<=>$b} keys %newdata) {
print OUT '>Contig'.$key, "\n", $newdata{$key},"\n";
}
close OUT;
unlink ($new_raw_ref);
}
sub final {
my ($fixed, $original, $final) = @_;
open (IN1, "<", $original);
open (IN2, "<", $fixed);
open (OUT,">", $final);
my %ori;
my %fix;
while (<IN1>) {
chomp (my $line = $_);
if ($line =~ m /^>/ ) {
chomp($ori{$line} = <IN1>);
}
}
close IN1;
while (<IN2>) {
chomp (my $line = $_);
if ($line =~ m /^>/ ) {
chomp ($fix{$line} = <IN2>);
}
}
close IN2;
my %newfix;
foreach my $line (keys %ori) {
if ($fix{$line}) {
if ((length ($fix{$line})) < (length ($ori{$line}))) {
my $diff = (length ($ori{$line})) - (length ($fix{$line}));
my $N = 'N' x $diff;
#print $line, "\n";
#print length ($fix{$line}), "\t", length ($ori{$line}), "\n";
my $newseq = $fix{$line}. $N;
#print $newseq, "\n";
$newfix {substr($line, 7)} = $newseq;
}
elsif ((length ($fix{$line})) > (length ($ori{$line}))) {
}
else {
$newfix {substr($line, 7)} = $fix{$line};
}
}
else {
$newfix{substr($line, 7)} = 'N' x length($ori{$line});
}
}
for my $key (sort {$a<=>$b} keys %newfix) {
print OUT '>Contig'.$key, "\n", $newfix{$key},"\n";
}
close OUT;
unlink ($fixed);
}
}
####################################################################################################################################################
sub MERGE {
die(qq/
Usage PopGenomics.pl MERGE [options]
Options: -a FILE .pos of population 1
-b FILE .pos of population 2
-c INT if 1 generate concensus, private SNPs are removed; if 2 combine two pos files including private and shared SNPs [2]
-o FILE outfile name
\n/) if (!@ARGV);
my %opts = (a=>undef, b=>undef, c=>2, o=>undef);
getopts('a:b:c:o:', \%opts);
open (IN1, "<", $opts{a}) or die ("\nError! .pos of population 1 is missing!\n\n") ;
open (IN2, "<", $opts{b}) or die ("\nError! .pos of population 2 is missing!\n\n") ;
open (OUT,">", $opts{o}) or die ("\nError! Must define the outfile!\n\n") ;
if ($opts{c} == 1) {
my %mod;
while (<IN1>) {
chomp (my @line = split /\t/, $_);
$mod{$line[0]}{$line[1]} = 1;
}
close IN1;
my %hist;
while (<IN2>) {
chomp (my @line2 = split /\t/, $_);
$hist{$line2[0]}{$line2[1]} = 1;
}
close IN2;
my %new;
foreach my $contig (sort {$a <=> $b} keys %hist){
foreach my $pos (sort {$a <=> $b} keys %{$hist{$contig}}) {
if ($mod{$contig}{$pos}) {
print OUT $contig, "\t", $pos, "\n";
}
}
}
close OUT;
}
if ($opts{c} == 2) {
system ("cat $opts{a} $opts{b} > merge");
open (IN1, "<", 'merge');
open (OUT,">", $opts{o});
my %mod;
while (<IN1>) {
chomp (my @line = split /\t/, $_);
$mod{$line[0]}{$line[1]} = 1;
}
close IN1;
my %new;
foreach my $contig (sort {$a <=> $b} keys %mod){
foreach my $pos (sort {$a <=> $b} keys %{$mod{$contig}}) {
print OUT $contig, "\t", $pos, "\n";
}
}
close OUT;
system ("rm merge");
}
}
####################################################################################################################################################
sub Structure {
die(qq/
Usage PopGenomics.pl Structure [options]
Options: -g FILE raw genotype probability generated using ANGSD "-doGeno 4" (e.g. Contig29 294 TT TT TA....)
-n INT sample size
-s INT number of loci
-o FILE outfile name
-h FILE Population information
-p if p is supplied, Random choose one SNP per contig.
\n/) if (!@ARGV);
my %opts = (g=>undef, n=>undef, s=>undef,o=>undef,h=>undef);
getopts('n:g:s:o:h:p', \%opts);
my %genos = ('AA' => 0 , 'AC' => 1, 'CA'=>1, 'AG' => 2, 'GA' => 2, 'AT' => 3, 'TA'=>3, 'CC'=> 4, 'CG'=>5, 'GC'=>5, 'CT' => 6, 'TC' => 6, 'GG'=>7, 'GT'=>8, 'TG'=>8, 'TT'=>9, 'NN' => -9);
# A = 1, C = 2, G = 3, T = 4
my %genos2 = ('0' => ['1','1'], '1' => ['1','2'], '2' => ['1','3'], '3' => ['1','4'], '4'=>['2','2'], '5'=>['2','3'], '6' => ['2','4'], '7'=>['3','3'], '8'=>['3','4'], '9'=>['4','4'], '-9' => ['-9','-9'] );
unless ($opts{p}) {
my $start0 = time;
my $out = 'cleaned';
trim($opts{n},$opts{s},$opts{g},$out,\%genos);
my $time0 = int(time - $start0);
print "Xixi...Trimmed original genotype matrix in $time0 sec!\n";
my $start1 = time;
my $out2= 'converted2';
transpose($out, $opts{n}, $opts{s}, $out2); #transpose the matrix;
my $time1 = int(time - $start1);
print "Hehe...Transposed cleaned genotype matrix in $time1 sec! \n";
my $start2 = time;
my $final = $opts{o};
convert($out2, $final, \%genos2); #convert the transposed matrix to input for STRUCTURE;
my $time2 = int(time - $start2);
print "Hoho... Converted transposed genotype matrix to STRUCTURE input in $time1 sec!\n";
}
if ($opts{p}) {
open (IN, "<", $opts{g});
my %hash;
my %hash1;
my $size = $opts{n};
open (OUT, ">", "selected");
foreach (<IN>) {
chomp (my @line = split /\s/, $_);
my $site = 0;
my $missing = 0;
my $hets = 0;
my @geno;
foreach my $m (@line[2..$#line]) {
if ($m ne 'NN') {
push (@geno, $genos{$m});
$site++;
}
if ($m eq 'NN') {
$site++; $missing++;
}
if ($m ne 'AA' && $m ne 'TT' & $m ne 'CC' && $m ne 'GG' && $m ne 'NN' ) {
$hets++;
}
}
my %seen;
my @unique = grep { ! $seen{$_}++ } @geno;
if ($hets > 0 ) {
if (scalar @unique <=3 && scalar @unique >= 2 && $site == $size && $missing/$site < 0.2) {
$hash{$line[0]}{$line[1]} = join ("\t",@line[2..$#line] );
}
}
if ($hets == 0) {
if ( scalar @unique == 2 && $site == $size && $missing/$site < 0.2) {
$hash{$line[0]}{$line[1]} = join ("\t",@line[2..$#line] );
}
}
}
close IN;
foreach (sort {$a cmp $b} keys %hash) {
my @array = ();
foreach my $pos (keys %{$hash{$_}}){
push (@array, $pos);
}
my $randomelement = $array[rand @array];
print OUT $_, "\t", $randomelement, "\t", join("\t",$hash{$_}{$randomelement}), "\n";
print $_, "\t", $randomelement, "\t", join("\t",$hash{$_}{$randomelement}), "\n";
}
close OUT;
open (IN2, "<", "selected");
my $n = 0;
foreach (<IN2>) {
chomp(my @line = split /\t/, $_);
$n++;
}
close IN2;
print "The number of selected sites now is: ", $n, "\n";
my $start0 = time;
my $out = 'cleaned';
trim($opts{n},$opts{s},"selected",$out,\%genos);
my $time0 = int(time - $start0);
print "Xixi...Trimmed original genotype matrix in $time0 sec!\n";
my $start1 = time;
my $out2= 'converted';
transpose($out, $opts{n}, $n, $out2); #transpose the matrix;
my $time1 = int(time - $start1);
print "Hehe...Transposed cleaned genotype matrix in $time1 sec! \n";
my $start2 = time;
my $final = $opts{o};
convert($out2, $final, \%genos2, $opts{h}); #convert the transposed matrix to input for STRUCTURE;
my $time2 = int(time - $start2);
print "Hoho... Converted transposed genotype matrix to STRUCTURE input in $time1 sec!\n";
}
sub trim{
my ($sample, $sites, $file, $out, $genos) = @_;
my %genos = %{$genos};
open (GENOPROB, '<', $file);
open (OUT, '>', $out);
foreach (<GENOPROB>) {
my @geno = split /\s+/, $_;
for (my $i = 2; $i<=$sample ;$i++) {
print OUT $genos{$geno[$i]}, "\t";
}
print OUT $genos{$geno[$sample+1]},"\n";
}
close GENOPROB;
close OUT;
#unlink ($file);
}
sub transpose {
my ($file, $size, $site1, $out) = @_;
open (OUT1, '>', $out);
for (my $i = 1; $i <= $size; $i++) {
my $count = $site1;
open (IN1, '<', $file);
foreach (<IN1>) {
chomp();
if ($count > 1) {
my @line = split /\s+/, $_;
print OUT1 $line[$i-1], "\t";
$count--;
}
elsif ($count == 1) {
my @line = split /\s+/, $_;
print OUT1 $line[$i-1], "\n";
}
else {
last;
}
}
}
close IN1;
close OUT1;
# unlink ($file);
}
sub convert {
my ($file, $final, $genos2,$pop) = @_;
my %genos2 = %{$genos2};
open (IN, '<', $file);
open (OUT,'>', $final);
open (POP, '<',$pop);
my $d = 1;
my %pop;
foreach (<POP>) {
chomp(my @line = split /\t/, $_);
$pop{$d} = $line[1];
$d++;
}
my $i = 1;
foreach (<IN>) {
my @array1;
my @array2;
chomp (my @line = split /\s+/, $_);
foreach my $gene (@line) {
push (@array1, "\t", $genos2{$gene}[0]);
}
print OUT $i, "\t", $pop{$i}, @array1, "\n";
foreach my $gene2 (@line) {
push (@array2, "\t",$genos2{$gene2}[1]);
}
print OUT $i,"\t", $pop{$i}, @array2, "\n";
$i++;
}
unlink ($file);
}
close OUT;
close IN;
}
####################################################################################################################################################
sub Admixture {
die(qq/
Usage PopGenomics.pl Admixture [options]
Options: -g FILE raw genotype probability generated using ANGSD "-doGeno 2" (e.g. Contig29 294 0 1 2 -1 -1 2 1....)
-o FILE outfile perfix
-p Randomly selects one snp per contig, kick off non-varibale sites
-n INT sample size (need -p)
\n/) if (!@ARGV);
my %opts = (g=>undef,o=>undef, n=>undef);
getopts('g:o:n:p', \%opts);
unless ($opts{p}) {
system ("sed 's/-1/9/g' $opts{g} > $opts{o}_converted");
open (IN, "<", $opts{o}. "_converted");
open (OUT, ">", $opts{o} . "_admixture.geno");
system ("rm $opts{o}_converted");
while (<IN>) {
chomp (my @line = split /\s+/, $_);
my $add = 0;
my $site = 0;
my $missing = 0;
foreach my $m (@line[2..$#line]) {
if ($m eq '2' || $m eq '1') {
$add++; $site++;
}
if ($m eq '0') {
$site++;
}
if ($m eq '9') {
$site++;$missing++;
}
}
if ($add > 0 && ($missing/$site <= 0.1)) {
print OUT @line[2..$#line],"\n";
}
}
close IN;
close OUT;
}
if ($opts{p}) {
system ("sed 's/-1/9/g' $opts{g} > $opts{o}_converted");
open (IN, "<", $opts{o} . "_converted");
my %hash;
my $size = $opts{n};
open (OUT, ">", $opts{o} . "_selected");
foreach (<IN>) {
chomp (my @line = split /\s/, $_);
my $add = 0;
my $site = 0;
foreach my $m (@line[2..$#line]) {
if ($m eq '2' || $m eq '1') {
$add++; $site++;
}
if ($m eq '0') {
$site++;
}
if ($m eq '9') {
$site++;
}
if ($add > 0 && $site == $size) {
$hash{$line[0]}{$line[1]} = join ("\t",@line[2..$#line] );
}
}
}
close IN;
foreach (sort {$a cmp $b} keys %hash) {
my @array = ();
foreach my $pos (keys %{$hash{$_}}){
push (@array, $pos);
}
my $randomelement = $array[rand @array];
print OUT $_, "\t", $randomelement, "\t", join("\t",$hash{$_}{$randomelement}), "\n";
}
close OUT;
open (OUT2, ">", $opts{o} . "_admixture.geno");
open (IN2, "<", $opts{o} . "_selected");
foreach (<IN2>) {
chomp(my @line = split /\t/, $_);
print OUT2 join('', @line[2..$#line]), "\n";
}
close IN2;
close OUT2;
system ("rm $opts{o}_selected $opts{o}_converted");
}
}
###################################################################################################################################################
sub Adegenet {
die(qq/
Usage PopGenomics.pl geno_to_adegenet [options]
Options: -g FILE raw genotype probability generated using ANGSD "-doGeno 2" (e.g. Contig29 294 0 1 2 -1 -1 2 1....)
-n INT sample size
-s INT number of loci
-o FILE outfile name
-h INT 1 = all sites; 0 = one snp per contig [1] ##only keep informative
-p Jason Bragg method for choosing SNPs: 1) Selects one snp per contig; 2) A SNP must have a genotype called in all samples; 3) It must be parsimony informative (minor allele present in > 1 sample) - note this has been modified below; 4) If multiple SNPs in a contig fulfil these criteria, one SNP is chosen at random. If -p is not used, all sites will be converted.
Note: you can only choose either -h or -p
\n/) if (!@ARGV);
my %opts = (g=>undef, n=>undef, s=>undef,o=>undef, h=>1);
getopts('n:g:s:o:h:p', \%opts);
my %geno_hash = ('-1' => ['N','A'], '0' => ['1','1'], '1' => ['1','2'], '2' => ['2','2']);
unless ($opts{p}) {
if ($opts{h} == 1 ) {
open (IN, "<", $opts{g});
my $out = 'trimmed';
open (OUT,">", $out);
foreach (<IN>) {
chomp (my @line = split /\s+/, $_);
my $add = 0;
my $site = 0;
my $missing = 0;
my @new;
foreach my $m (@line[2..$#line]) {
if ($m eq '2' || $m eq '1') {
$add++; $site++;
}
if ($m eq '0') {
$site++;
}
if ($m eq '-1') {
$site++; $missing++;
}
my $gene = $geno_hash{$m}[0] . $geno_hash{$m}[1];
push (@new, $gene);
}
if ($add > 1 && ($missing/$site <= 0.2)) {
print OUT join ("\t", @new),"\n";
}
}
close IN;
close OUT;
open (IN2,"<", $out);
my $add;
while (<IN2>) {
$add++;
}
close IN2;
#trimmed ($opts{g},'trimmed' ,$opts{n}, \%geno_hash);
transpose('trimmed', $opts{n}, $add, 'transposed'); #transpose the matrix;
adegenet('transposed', $opts{s}, $opts{o});
}
if ($opts{h} == 0 ) {
open (IN, "<", $opts{g});
my %hash;
my $size = $opts{n};
open (OUT, ">", "selected");
foreach (<IN>) {
chomp (my @line = split /\s/, $_);
my $add = 0;
my $site = 0;
my $missing = 0;
foreach my $m (@line[2..$#line]) {
if ($m eq '2' || $m eq '1') {
$add++; $site++;
}
if ($m eq '0') {
$site++;
}
if ($m eq '-1') {
$site++; $missing++;
}
if ($add > 1 && $site == $size && ($missing/$site <= 0.2)) {
$hash{$line[0]}{$line[1]} = join ("\t",@line[2..$#line] );
}
}
}
close IN;
foreach (sort {$a cmp $b} keys %hash) {
my @array = ();
foreach my $pos (keys %{$hash{$_}}){
push (@array, $pos);
}
my $randomelement = $array[rand @array];
print OUT $_, "\t", $randomelement, "\t", join("\t",$hash{$_}{$randomelement}), "\n";
}
close OUT;
open (IN2, "<", "selected");
my $n = 0;
foreach (<IN2>) {
chomp(my @line = split /\t/, $_);
$n++;
}
close IN2;
print "The number of selected sites now is: ", $n, "\n";
trimmed ('selected','trimmed' ,$opts{n}, \%geno_hash);
system("rm selected");
transpose('trimmed', $opts{n}, $n, 'transposed'); #transpose the matrix;
adegenet('transposed', $n, $opts{o});
}
sub trimmed {
my ($geno, $trim, $sample, $geno_hash) = @_;
my %geno_hash = %{$geno_hash};
open (IN, '<', $geno);
open (TRIM, '>',$trim);
foreach (<IN>) {
my $count = 1;
chomp(my @line = split /\s+/, $_);
foreach (@line[2..$#line]) {
chomp();
if ($count < $sample) {
$count++;
print TRIM $geno_hash{$_}[0] . $geno_hash{$_}[1], "\t";
}
elsif ($count == $sample) {
print TRIM $geno_hash{$_}[0] . $geno_hash{$_}[1], "\n";
}
}
}
close IN;
close TRIM;
}
sub adegenet {
my ($in, $sites, $out) = @_;
open (IN2, "<", $in);
open (OPTo, '>', $out);
my $count = 1;
for ($count = 1; $count <= $sites; $count++) {
print OPTo "\t", join ("", "Loc". $count);
}
print OPTo "\n";
open (IN2, '<', 'transposed');
$count = 1;
foreach (<IN2>) {
print OPTo 'Ind'.$count, "\t", join ("", $_);
$count++;
}
unlink ($in);
close OPTo;
close IN2;
}
}
if ($opts{p}) {
jasonBragg ($opts{g}, $opts{n}, 'out.JB.original',$opts{o}, \%geno_hash, $opts{s});
}
sub jasonBragg {
my ($file, $size, $out, $final, $geno_hash, $snps) = @_;
my %geno_hash = %{$geno_hash};
my %hash;
open (IN, '<', $file);
open (OUT, '>', $out);
foreach (<IN>) {
my @line = split /\s/, $_;
my $add = 0;
my $site = 0;
foreach my $m (@line[2..$#line]) {
if ($m eq '2' || $m eq '1') {
$add++; $site++;
}
if ($m eq '0') {
$site++;
}
if ($add >= 2 ) { ## && $site == $size removed
$hash{$line[0]}{$line[1]} = join ("\t",@line[2..$#line] );
}
}
}
close IN;
foreach (sort {$a cmp $b} keys %hash) {
my @array = ();
foreach my $pos (keys %{$hash{$_}}){
push (@array, $pos);
}
my $randomelement = $array[rand @array];
print OUT $_, "\t", $randomelement, "\t", join("\t",$hash{$_}{$randomelement}), "\n";
}
close OUT;
trimmed ('out.JB.original','trimmed', $size, \%geno_hash);
my $j=0;
open (STUPID, "<", 'out.JB.original');
foreach (<STUPID>) {
$j++;
}
transpose('trimmed', $size, $j, 'transposed'); #transpose the matrix;
adegenet('transposed', $j, $final);
}
}
####################################################################################################################################################
sub PCA {
die(qq/
Usage PopGenomics.pl PCA [options]
Options: -g FILE raw genotype probability generated using ANGSD "-doGeno 32"
-w INT weighting or no weighting? if INT=1 weighting, if INT=2 no weighting [2]
-i INT if no weighting, the minimal minor allele frequency cutoff, requires w=2
-z INT file with SFS posterior probabilities [required if you want to weight each site by its probability of being variable], this is the binary output of sfstools after running ANGSD realSFS1 and optimSFS
-s INT number of sites to be analyzed
-n INT number of samples
-b INT block size
-m INT 0 or 1 normalizations for the estimate of the 'covariance' matrix for PCA [0]
-o FILE outfile name
\n/) if (!@ARGV);
my %opts = (g=>undef, w=>2, i=>undef,s=>undef, N=>undef, b=>undef, m=>0, o=>undef,z=>undef);
getopts('g:w:i:s:n:b:m:o:z:', \%opts);
if ($opts{w} == 2) {
die(qq/
option -i (minimal minor allele frequency cutoff) is required
\n/) unless ($opts{i});
}
if ($opts{w} == 1) {
die(qq/
option -z (SFS posterior probabilities) is required
\n/) unless ($opts{z});
}
my $ngsCovar = 'ngsCovar';
if ($opts{w} == 2) {
system (" $ngsCovar -probfile $opts{g} -outfile $opts{o} -nind $opts{n} -nsites $opts{s} -verbose 0 -block_size $opts{b} -norm $opts{m} -minmaf $opts{i}");
}
if ($opts{w} == 1) {
system (" $ngsCovar -probfile $opts{g} -outfile $opts{o} -nind $opts{n} -nsites $opts{s} -verbose 0 -block_size $opts{b} -norm $opts{m} -sfsfile $opts{z}");
}
}
####################################################################################################################################################
sub ANGSD {
die(qq/
Usage PopGenomics.pl ANGSD [options]
Options:
Basic:
-b FILE a file that contains names (and paths) of all BAM files (alignment) generated by the SamTools
-f FILE a file that contains all sites to keep, file must end by ".keep"
-r FILE reference fasta file used to align reads and generate BAM alignment files listed in a file after "-b"
-a FILE ancestral file, if no ancestral file then just use reference fasta file for -a
-F INT 1=folded 0=unfolded [1]. You have to do folded if an ancestral fasta is unavailable
-Q INT minimal Phred quality score to keep a base [20]
-q INT minimal map quality [0]
-t INT number of threads [4]
-g INT genotype output options [2]
1 = print out major minor
2 = print the called genotype as 0,1,2 (used by Format_converter.pl PCA)
4 = print the called genotype as AA, AC, AG, ... (used by PopGenomics.pl geno_to_structure)
8 = print all 3 posts (major,major),(major,minor),(minor,minor)
16 = print the posterior of the called genotype
32 = somewhat different dumps the binary posterior for all samples, encoded as 3*nind double
64 = all above
-n INT sample size
-o INT outfile Prefix
Theta Estimate:
-T estimating per-site thetas? [null]
SNP\/Genotype calling:
-c INT 1 = call genotypes; 0 = no [0]
-s INT 1 = call SNPs; 0 = no [0]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
if c = 1
-P FLOAT Posterior prob cutoff for calling genotypes [0.95]
-e INT 1 = estimate the posterior genotype probability based on the allele frequency as a prior
2 = estimate the posterior genotype probability assuming a uniform prior
[1]
-h INT min depth to call genotypes [0]
-d INT Discard site if effective sample size below value. 0 indicates no filtering [0]