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pogenom.pl
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pogenom.pl
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#!/usr/bin/perl -w
=head1 NAME
pogenom.pl - Calculates population genomic parameters from a VCF file
=head1 USAGE (minimum input)
Either:
perl pogenom.pl --vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --genome_size GENOME_SIZE [--help]
Or:
perl pogenom.pl --vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --gff_file GFF_FILE [--help]
Or:
perl pogenom.pl --vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --fasta_file FASTA_FILE [--help]
=head1 REQUIRED ARGUMENTS
--vcf_file VCF_FILE Specify vcf file with data from a single or multiple samples
--out OUTPUT_FILES_PREFIX Specify the prefix of the output file name(s) (overwrites existing files with same names)
--genome_size GENOME_SIZE Specify genome size (in bp; integer). Not required if --gff_file or --fasta_file with genome sequence is given
=head1 OPIONAL ARGUMENTS
--gff_file GFF_FILE Specify gff file. Either this, --genome_size or --fasta_file must be given
--fasta_file FASTA_FILE Specify fasta file. Either this, --genome_size or --gff_file must be given
--genetic_code_file GENETIC_CODE_FILE Specify genetic code file. E.g. standard_genetic_code.txt in the POGENOM distribution
--loci_file LOCI_FILE Specify file with ids of loci to be included
--min_count MIN_COUNT Specify minimum coverage for a locus to be included for the sample
--min_found MIN_FOUND_IN Specify minimum number of samples that a locus needs to be present in to be included
--subsample SUBSAMPLE Specify coverage level at which to subsample
--keep_haplotypes If this is used, POGENOM will not split haplotypes into single-nucleotide variants, which is otherwise the default
--vcf_format Specify VCF file format version. Can be set to freebayes (default) or GATK
--help Prints this help message
[Press q to close this help message]
=cut
use Getopt::Long;
use List::MoreUtils qw(uniq);
$genome_size = undef;
$min_found_in = 1;
$min_count = 2;
$vcf_file = undef;
$gff_file = undef;
$fasta_file = undef;
$genetic_code_file = undef;
$outprefix = undef;
$reference = undef;
$keep_haplotypes = undef;
$use_pseudocounts = undef;
$subsample = undef;
$vcf_format = "freebayes";
$na_if_missing_loci = 1;
&GetOptions('vcf_file=s' => \$vcf_file, 'vcf_format=s' => \$vcf_format, 'gff_file=s' => \$gff_file, 'fasta_file=s' => \$fasta_file, 'genetic_code_file=s' => \$genetic_code_file, 'output=s' => \$outprefix, 'min_count=i' => \$min_count, 'min_found=i' => \$min_found_in, 'ref=s' => \$reference, 'genome_size=i' => \$genome_size, 'keep_haplotypes!' => \$keep_haplotypes, 'loci_file=s' => \$loci_file, 'subsample=s' => \$subsample, 'use_pseudocounts' => \$use_pseudocounts, 'h!' => \$help);
if (!$outprefix) {
system ('perldoc', $0);
exit;
}
if ($help) {
system ('perldoc', $0);
exit;
}
if (!$vcf_file) {
system ('perldoc', $0);
exit;
}
if (!$genome_size and !$gff_file and !$fasta_file) {
system ('perldoc', $0);
exit;
}
if ($min_count < 2) {
print"Error: min_count cannot be set to <2\n";
exit;
}
if ($vcf_format ne "freebayes") {
if ($vcf_format ne "GATK") {
print"\nError: Unrecognized vcf_format. Should be either freebayes (default) or GATK\n\n";
exit;
}
}
####################
print"\n### Running pogenom ###\n";
if ($genome_size) {
print"genome_size set to $genome_size\n";
} elsif ($fasta_file) {
print"genome_size will be calculated from sequence file\n";
} elsif ($gff_file) {
print"genome_size will be calculated from GFF file\n";
}
print"min_count set to $min_count\n";
print"min_found set to $min_found_in\n";
if ($subsample) {
print"Subsampling will be done with $subsample reads per sample\n";
}
if ($loci_file) {
print"Analysis restricted to loci in file: $loci_file\n";
&read_loci_to_include;
}
print"\n### Read variant data ###\n";
if ($keep_haplotypes) {
&get_snp_data_combined_vcf;
} else {
&get_snp_data_combined_vcf_split_haplotypes;
}
if ($subsample) {
&subsample_allele_counts;
#&subsample_allele_counts_dupl;
}
if ($gff_file) {
print"\n### Reading GFF file ###\n";
&read_gff;
}
if ($fasta_file) {
print"\n### Reading fasta sequence file ###\n";
&read_fasta;
}
if ($genetic_code_file) {
print"\n### Reading Genetic Code file ###\n";
&read_genetic_code;
}
print"\n### Calculating Nucleotide Diversity (pi) ###\n";
&calc_pi;
if ($gff_file) {
print"\n### Calculating Gene-wise Nucleotide Diversity (pi) ###\n";
&calc_per_gene_pi;
if ($genetic_code_file) {
print"\n### Calculating Gene-wise Aminoacid Diversity (aa-pi) ###\n";
&calc_per_gene_aminoacid_pi;
print"\n### Calculating Gene-wise pN/pS ###\n";
&calc_pN_pS;
}
}
if (@samples > 1) {
print"\n### Calculating Fixation Index (FST) ###\n";
&calc_fst;
if ($gff_file) {
print"\n### Calculating Gene-wise Fixation Index (FST) ###\n";
&calc_per_gene_fst;
if ($genetic_code_file) {
print"\n### Calculating Gene-wise Aminoacid Fixation Index (aa-FST) ###\n";
&calc_per_gene_aminoacid_fst;
}
}
}
print"\n### Printing results to files ###\n";
&print_output_to_file;
print"\n### Finished pogenom succesfully ###\n\n";
####################
sub read_loci_to_include {
open (INFILE, "$loci_file") || die ("Error: can't open $loci_file");
while (<INFILE>) {
chomp;
$row = $_;
@fields = split(/\t/, $row);
$locus = $fields[0]."|".$fields[1];
$include_locus{$locus} = 1;
#print"$locus\n";
}
$temp = keys %include_locus;
print"Number of loci specified in file: $temp\n";
}
sub read_gff {
$fasta_started = 0;
$seq = "";
open (INFILE, "$gff_file") || die ("Error: can't open $gff_file");
print"Reading $gff_file\n";
while (<INFILE>) {
chomp;
$row = $_;
#print"$row\n";
if ($fasta_started == 1) {
if (substr($row, 0, 1) eq ">") {
if ($seq ne "") {
$contig_seq{$contig} = $seq;
}
$contig = $row;
substr($contig, 0, 1) = "";
$seq = "";
} else {
$seq = $seq.$_;
$contig_seq{$contig} = uc $seq;
}
}
elsif (substr($row, 0, 7) eq "##FASTA") {
$fasta_started = 1;
} else {
next if (substr($row, 0, 1) eq "#");
@fields = split(/\t/, $row);
next if (@fields == 1);
$contig = $fields[0];
$start = $fields[3];
$end = $fields[4];
$strand = $fields[6];
$end = $end - 3 if ($strand eq "+"); # to exclude the stop codon
$start = $start + 3 if ($strand eq "-"); # to exclude the stop codon
$annotation = $fields[8];
@subfields = split(/;/, $annotation);
$gene = $subfields[0];
if (defined $gene_start{$gene}) {
print"Error: Non-unique gene identifiers in GFF file. The program will exit without finishing.\n\n"; exit;
}
$gene_start{$gene} = $start;
$gene_end{$gene} = $end;
$gene_strand{$gene} = $strand;
$gene_length{$gene} = $gene_end{$gene} - $gene_start{$gene} + 1;
$gene_contig{$gene} = $contig;
if (!defined $contig_genes{$contig}) {
push(@contigs, $contig);
}
push(@{ $contig_genes{$contig} }, $gene);
for ($pos = $start; $pos < $end; $pos++) {
$locus = $contig."|".$pos;
#print"$locus#\n";
if (defined $locus_found{$locus}) {
if ($locus_found{$locus} >= $min_found_in) {
$gene_locus{$gene}{$locus} = 1;
}
}
}
}
}
close (INFILE);
if ($fasta_started == 1) {
$temp_genome_size = 0;
foreach $contig (@contigs) {
$temp_genome_size = $temp_genome_size + length($contig_seq{$contig});
@genes = @{ $contig_genes{$contig} };
foreach $gene (@genes) {
if ($gene_strand{$gene} eq "+") {
$gene_seq{$gene} = substr($contig_seq{$contig}, ($gene_start{$gene} - 1), $gene_length{$gene});
#$peptide = "";
#for ($j = 0; $j < $gene_length{$gene}; $j=$j+3) {
# $codon = substr($gene_seq{$gene}, $j, 3);
# $peptide = $peptide.$codon_aminoacid{$codon};
#}
#print">$gene\n$gene_seq{$gene}\n";
#print">$gene\n$peptide\n";
}
if ($gene_strand{$gene} eq "-") {
$gene_seq{$gene} = substr($contig_seq{$contig}, ($gene_start{$gene} - 1), $gene_length{$gene});
$gene_seq{$gene} = &make_revcomp($gene_seq{$gene});
#$peptide = "";
#for ($j = 0; $j < $gene_length{$gene}; $j=$j+3) {
# $codon = substr($gene_seq{$gene}, $j, 3);
# $peptide = $peptide.$codon_aminoacid{$codon};
#}
#print">$gene\n$gene_seq{$gene}\n";
#print">$gene\n$peptide\n";
}
}
}
}
if (!$genome_size and !$fasta_file) {
if ($fasta_started == 1) {
$genome_size = $temp_genome_size;
print"Genome size calculated from GFF to $genome_size bp\n";
} else {
print"Error: Genome size could not be calculated from GFF file\n\n"; exit;
}
}
}
sub read_fasta {
%contig_seq = ();
$seq = "";
open (INFILE, "$fasta_file") || die ("Error: can't open $fasta_file");
print"Reading $fasta_file\n";
while (<INFILE>) {
chomp;
$row = $_;
if (substr($row, 0, 1) eq ">") {
if ($seq ne "") {
$contig_seq{$contig} = $seq;
}
$contig = $row;
#@subfields = split(/\s+/, $row);
#$contig = $subfields[0];
substr($contig, 0, 1) = "";
$seq = "";
} else {
$seq = $seq.$_;
$contig_seq{$contig} = uc $seq;
}
}
if (!$genome_size) {
$genome_size = 0;
foreach $contig (keys %contig_seq) {
$genome_size = $genome_size + length($contig_seq{$contig});
}
}
print"Genome size calculated from sequence file to $genome_size bp\n";
if (defined $gff_file) {
foreach $contig (@contigs) {
if (!defined $contig_seq{$contig}) {
print"\nError: Missmatch between contig id in gff and sequence file\n\n"; exit;
}
@genes = @{ $contig_genes{$contig} };
foreach $gene (@genes) {
if ($gene_strand{$gene} eq "+") {
$gene_seq{$gene} = substr($contig_seq{$contig}, ($gene_start{$gene} - 1), $gene_length{$gene});
}
if ($gene_strand{$gene} eq "-") {
$gene_seq{$gene} = substr($contig_seq{$contig}, ($gene_start{$gene} - 1), $gene_length{$gene});
$gene_seq{$gene} = &make_revcomp($gene_seq{$gene});
}
}
}
}
}
sub read_genetic_code {
open(INFILE, "$genetic_code_file") || die ("Error: can't open $genetic_code_file");
print"Reading $genetic_code_file\n";
while (<INFILE>) {
chomp;
@fields = split(/\t/);
$codon_aminoacid{$fields[0]} = $fields[1];
#print"#$fields[0]#$fields[1]#\n";
}
close (INFILE);
}
sub get_snp_data_combined_vcf {
%nt = ('A', 1, 'T', 1, 'C', 1, 'G', 1);
@samples = ();
@samples_plus = ();
open (INFILE, "$vcf_file") || die ("Error: can't open $vcf_file");
print"Reading $vcf_file\n";
while (<INFILE>) {
#chomp;
$_ =~ s/\R//g;
$row = $_;
@fields = split(/\t/, $row);
if (substr($row, 0, 6) eq "#CHROM") {
for ($i = 9; $i < @fields; $i++) {
$samples[$i - 9] = $fields[$i];
}
@samples_plus = (@samples, 'All_samples_combined');
}
next if (substr($row, 0, 1) eq "#");
#next if (@fields == 1);
$contig = $fields[0];
$pos = $fields[1];
$locus = $contig."|".$pos;
#print"$locus $locus_found{$locus} $min_found_in\n";
if ($loci_file) {
#print"$locus\n";
next if (!defined $include_locus{$locus});
}
@subfields = split(/:/, $fields[8]);
$nformat_fields = @subfields;
if ($vcf_format eq "GATK") {
$count_ix = undef;
for ($i = 0; $i < @subfields; $i++) {
$count_ix = $i if ($subfields[$i] eq "AD");
}
if (!$count_ix) {
print"\nError: Field AD is lacking in the Format column of the VCF file at CHROM: $contig POS: $pos\n\n"; exit;
}
} elsif ($vcf_format eq "freebayes") {
$tot_count_ix = $ref_count_ix = $alt_count_ix = undef;
for ($i = 0; $i < @subfields; $i++) {
#$tot_count_ix = $i if ($subfields[$i] eq "DP");
$ref_count_ix = $i if ($subfields[$i] eq "RO");
$alt_count_ix = $i if ($subfields[$i] eq "AO");
}
if (!$ref_count_ix or !$alt_count_ix) {
print"\nError: Either field RO or AO is lacking in the Format column of the VCF file at CHROM: $contig POS: $pos\n\n"; exit;
}
}
$locus_found{$locus} = 0;
for ($i = 9; $i < @fields; $i++) {
@subfields = split(/:/, $fields[$i]);
if (@subfields == $nformat_fields) {
if ($vcf_format eq "GATK") {
@allele_count = split(/,/, $subfields[$count_ix]);
} elsif ($vcf_format eq "freebayes") {
@allele_count = split(/,/, $subfields[$alt_count_ix]);
unshift(@allele_count, $subfields[$ref_count_ix]);
}
if ($allele_count[0] ne ".") {
$tot_count = 0;
for ($j = 0; $j < @allele_count; $j++) {
$tot_count = $tot_count + $allele_count[$j];
}
if ($tot_count >= $min_count) {
$locus_found{$locus}++;
#print"$locus_found{$locus}\n";
}
}
}
}
next if ($locus_found{$locus} < $min_found_in);
$contig_pos{$contig}{$pos} = 1;
$ref = $fields[3];
@alleles = split(/,/, $fields[4]);
unshift(@alleles, $ref);
$sample_locus_totcount{'All_samples_combined'}{$locus} = 0;
for ($i = 9; $i < @fields; $i++) {
$sample = $samples[$i - 9];
@subfields = split(/:/, $fields[$i]);
next if (@subfields != $nformat_fields);
if ($vcf_format eq "GATK") {
@allele_count = split(/,/, $subfields[$count_ix]);
} elsif ($vcf_format eq "freebayes") {
@allele_count = split(/,/, $subfields[$alt_count_ix]);
unshift(@allele_count, $subfields[$ref_count_ix])
}
$tot_count = 0;
if ($allele_count[0] ne ".") {
for ($j = 0; $j < @allele_count; $j++) {
$tot_count = $tot_count + $allele_count[$j];
}
}
next if ($allele_count[0] eq ".");
next if ($tot_count < $min_count);
$sample_locus_ref{$sample}{$locus} = $ref;
$sample_locus_totcount{$sample}{$locus} = $tot_count;
$sample_locus_totcount{'All_samples_combined'}{$locus} = $sample_locus_totcount{'All_samples_combined'}{$locus} + $tot_count;
#print"Ref: #$ref# $ref_count\n";
for ($j = 0; $j < @alleles; $j++) {
$sample_locus_allel_counts{$sample}{$locus}{$alleles[$j]} = $allele_count[$j];
$sample_locus_allel_counts{'All_samples_combined'}{$locus}{$alleles[$j]} = 0 if (!defined $sample_locus_allel_counts{'All_samples_combined'}{$locus}{$alleles[$j]});
$sample_locus_allel_counts{'All_samples_combined'}{$locus}{$alleles[$j]} = $sample_locus_allel_counts{'All_samples_combined'}{$locus}{$alleles[$j]} + $allele_count[$j];
}
}
foreach $string (@alleles) {
$contig_pos{$contig}{$pos} = 0 if (!defined $nt{$string});
}
}
foreach $locus (keys %locus_found) {
$found[$locus_found{$locus}]++;
}
for ($i = 1; $i < @found; $i++) {
if (defined $found[$i]) {
print"Number of loci found $i times: $found[$i]\n"
} else {
print"Number of loci found $i times: 0\n"
}
}
}
sub get_snp_data_combined_vcf_split_haplotypes {
%nt = ('A', 1, 'T', 1, 'C', 1, 'G', 1);
@samples = ();
@samples_plus = ();
open (INFILE, "$vcf_file") || die ("Error: can't open $vcf_file");
print"Reading $vcf_file\n";
print"Haplotypes will be split into individual bases\n";
while (<INFILE>) {
#chomp;
$_ =~ s/\R//g;
$row = $_;
@fields = split(/\t/, $row);
if (substr($row, 0, 6) eq "#CHROM") {
for ($i = 9; $i < @fields; $i++) {
$samples[$i - 9] = $fields[$i];
}
@samples_plus = (@samples, 'All_samples_combined');
}
next if (substr($row, 0, 1) eq "#");
$contig = $fields[0];
$pos = $fields[1];
$ref = $fields[3];
@alleles = split(/,/, $fields[4]);
unshift(@alleles, $ref);
$indel = undef;
for ($i = 1; $i < @alleles; $i++) {
if (length($alleles[$i]) != length($ref)) {
$indel = 1;
}
}
next if $indel;
#print"Ref: $ref Alt: @alt\n";
@subfields = split(/:/, $fields[8]);
$nformat_fields = @subfields;
if ($vcf_format eq "GATK") {
$count_ix = undef;
for ($i = 0; $j < @subfields; $i++) {
$count_ix = $i if ($subfields[$i] eq "AD");
}
if (!$count_ix) {
print"\nError: Field AD is lacking in the Format column of the VCF file at CHROM: $contig POS: $pos\n\n"; exit;
}
} elsif ($vcf_format eq "freebayes") {
$tot_count_ix = $ref_count_ix = $alt_count_ix = undef;
for ($i = 0; $i < @subfields; $i++) {
#$tot_count_ix = $i if ($subfields[$i] eq "DP");
$ref_count_ix = $i if ($subfields[$i] eq "RO");
$alt_count_ix = $i if ($subfields[$i] eq "AO");
}
if (!$ref_count_ix or !$alt_count_ix) {
print"\nError: Either field RO or AO is lacking in the Format column of the VCF file at CHROM: $contig POS: $pos\n\n"; exit;
}
}
for ($i = 0; $i < length($ref); $i++) {
$modpos = $pos + $i;
$locus = $contig."|".$modpos;
if ($loci_file) {
next if (!defined $include_locus{$locus});
}
$locus_found{$locus} = 0;
for ($j = 9; $j < @fields; $j++) {
@subfields = split(/:/, $fields[$j]);
if (@subfields == $nformat_fields) {
if ($vcf_format eq "GATK") {
@allele_count = split(/,/, $subfields[$count_ix]);
} elsif ($vcf_format eq "freebayes") {
@allele_count = split(/,/, $subfields[$alt_count_ix]);
unshift(@allele_count, $subfields[$ref_count_ix]);
}
if ($allele_count[0] ne ".") {
$tot_count = 0;
for ($k = 0; $k < @allele_count; $k++) {
$tot_count = $tot_count + $allele_count[$k];
}
if ($tot_count >= $min_count) {
$locus_found{$locus}++;
}
}
}
}
next if ($locus_found{$locus} < $min_found_in);
$contig_pos{$contig}{$modpos} = 1;
$subref = substr($ref, $i, 1);
$contig_pos{$contig}{$modpos} = 0 if (!defined $nt{$subref});
$sample_locus_totcount{'All_samples_combined'}{$locus} = 0;
for ($j = 9; $j < @fields; $j++) {
$sample = $samples[$j - 9];
@subfields = split(/:/, $fields[$j]);
next if (@subfields != $nformat_fields);
if ($vcf_format eq "GATK") {
@allele_count = split(/,/, $subfields[$count_ix]);
} elsif ($vcf_format eq "freebayes") {
@allele_count = split(/,/, $subfields[$alt_count_ix]);
unshift(@allele_count, $subfields[$ref_count_ix])
}
$tot_count = 0;
if ($allele_count[0] ne ".") {
for ($k = 0; $k < @allele_count; $k++) {
$tot_count = $tot_count + $allele_count[$k];
}
}
next if ($allele_count[0] eq ".");
next if ($tot_count < $min_count);
$sample_locus_ref{$sample}{$locus} = $subref;
$sample_locus_totcount{$sample}{$locus} = $tot_count;
$sample_locus_totcount{'All_samples_combined'}{$locus} = $sample_locus_totcount{'All_samples_combined'}{$locus} + $tot_count;
#print" Sample: $sample Subpos: $i Modpos: $modpos\n";
#print" Subref: $subref $ref_count\n";
for ($k = 0; $k < @alleles; $k++) {
$subal = substr($alleles[$k], $i, 1);
if (defined $sample_locus_allel_counts{$sample}{$locus}{$subal}) {
$sample_locus_allel_counts{$sample}{$locus}{$subal} = $sample_locus_allel_counts{$sample}{$locus}{$subal} + $allele_count[$k];
} else {
$sample_locus_allel_counts{$sample}{$locus}{$subal} = $allele_count[$k];
}
$sample_locus_allel_counts{'All_samples_combined'}{$locus}{$subal} = 0 if (!defined $sample_locus_allel_counts{'All_samples_combined'}{$locus}{$subal});
$sample_locus_allel_counts{'All_samples_combined'}{$locus}{$subal} = $sample_locus_allel_counts{'All_samples_combined'}{$locus}{$subal} + $allele_count[$k];
$contig_pos{$contig}{$modpos} = 0 if (!defined $nt{$subal});
#print" Subal: $subal $allele_count[$k] $sample_locus_allel_counts{$sample}{$locus}{$subal}\n";
}
}
}
}
foreach $locus (keys %locus_found) {
$found[$locus_found{$locus}]++;
}
$temp = 0;
for ($i = 1; $i < @found; $i++) {
if (defined $found[$i]) {
$temp = 1;
print"Number of loci found $i times: $found[$i]\n"
} else {
print"Number of loci found $i times: 0\n"
}
}
#if ($temp == 0) {
if ((keys %sample_locus_allel_counts) == 0) {
print"Zero loci found fulfilling criteria\n";
print"No files will be generated\n";
exit;
}
}
sub subsample_allele_counts {
foreach $sample (@samples_plus) {
foreach $locus (keys %{$sample_locus_allel_counts{$sample}}) {
if ($sample_locus_totcount{$sample}{$locus} > $subsample) {
@alleles = (keys %{$sample_locus_allel_counts{$sample}{$locus}});
@temp = ();
foreach $allele (@alleles) {
$count = $sample_locus_allel_counts{$sample}{$locus}{$allele};
for ($i = 0; $i < $count; $i++) {
push(@temp, $allele);
}
$sample_locus_allel_counts{$sample}{$locus}{$allele} = 0;
}
for ($i = 0; $i < $subsample; $i++) {
$ix = int(rand(@temp));
$sample_locus_allel_counts{$sample}{$locus}{$temp[$ix]}++;
}
$sample_locus_totcount{$sample}{$locus} = $subsample;
}
}
}
}
sub subsample_allele_counts_dupl {
foreach $sample (@samples_plus) {
$sample_dupl = $sample."_duplicate";
push(@samples_plus_dupl, $sample);
push(@samples_plus_dupl, $sample_dupl);
foreach $locus (keys %{$sample_locus_allel_counts{$sample}}) {
if ($sample_locus_totcount{$sample}{$locus} > $subsample) {
@alleles = (keys %{$sample_locus_allel_counts{$sample}{$locus}});
@temp = ();
foreach $allele (@alleles) {
$count = $sample_locus_allel_counts{$sample}{$locus}{$allele};
for ($i = 0; $i < $count; $i++) {
push(@temp, $allele);
}
$sample_locus_allel_counts{$sample}{$locus}{$allele} = 0;
$sample_locus_allel_counts{$sample_dupl}{$locus}{$allele} = 0;
}
for ($i = 0; $i < $subsample; $i++) {
$ix = int(rand(@temp));
$sample_locus_allel_counts{$sample}{$locus}{$temp[$ix]}++;
}
for ($i = 0; $i < $subsample; $i++) {
$ix = int(rand(@temp));
$sample_locus_allel_counts{$sample_dupl}{$locus}{$temp[$ix]}++;
}
$sample_locus_totcount{$sample}{$locus} = $subsample;
$sample_locus_totcount{$sample_dupl}{$locus} = $subsample;
}
}
}
@samples = @samples_plus = @samples_plus_dupl;
}
sub calc_pi {
print "Sample\tpi\tTotal_num_loci\tTotal_num_alleles\tAverage_depth\n";
foreach $sample (@samples_plus) {
$intra_pi = 0;
$tot_alleles = 0;
$av_count = 0;
@loci = (keys %{$sample_locus_allel_counts{$sample}});
foreach $locus (@loci) {
$tot_count = $sample_locus_totcount{$sample}{$locus};
#print"Locus totcount $locus $tot_count\n";
@alleles = (keys %{$sample_locus_allel_counts{$sample}{$locus}});
#print"Alleles: @alleles\n";
$av_count = $av_count + $tot_count;
$locus_intra_pi = 0;
for ($i = 0; $i < @alleles; $i++) {
#print"Allele 1: $alleles[$i]\n";
$counts_1 = $sample_locus_allel_counts{$sample}{$locus}{$alleles[$i]};
#print"Counts1: $counts_1\n";
$tot_alleles++ if ($counts_1 > 0);
for ($j = 0; $j < @alleles; $j++) {
next if ($alleles[$i] eq $alleles[$j]);
#print"Allele 2: $alleles[$j]\n";
$counts_2 = $sample_locus_allel_counts{$sample}{$locus}{$alleles[$j]};
#print"Counts2: $counts_2\n";
$locus_intra_pi = $locus_intra_pi + ($counts_1/$tot_count)*($counts_2/($tot_count - 1)); # According to Schloising
#$locus_intra_pi = $locus_intra_pi + ($counts_1/$tot_count)*($counts_2/($tot_count)); # According to our initial version
}
}
#print"$locus $locus_intra_pi\n\n";
$sample_locus_pi{$sample}{$locus} = $locus_intra_pi;
$intra_pi = $intra_pi + $locus_intra_pi;
}
$intra_pi = $intra_pi/$genome_size;
$sample_pi{$sample} = $intra_pi;
$av_count = $av_count/@loci;
$sample_avcount{$sample} = $av_count;
$sample_totalleles{$sample} = $tot_alleles;
$num_loci{$sample} = @loci;
print "$sample\t$intra_pi\t$num_loci{$sample}\t$tot_alleles\t$av_count\n";
}
}
sub calc_per_gene_pi {
foreach $contig (@contigs) {
#print "$contig\n";
@genes = @{ $contig_genes{$contig} };
#print "@genes\n"; die;
foreach $gene (@genes) {
foreach $sample (@samples_plus) {
$intra_pi = 0;
$missing_loci = 0;
foreach $locus (keys %{$gene_locus{$gene}}) {
#print "$locus/n";
$missing_loci = 1 if (!defined $sample_locus_pi{$sample}{$locus});
next if (!defined $sample_locus_pi{$sample}{$locus});
$intra_pi = $intra_pi + $sample_locus_pi{$sample}{$locus};
}
$intra_pi = $intra_pi/$gene_length{$gene};
$sample_gene_pi{$sample}{$gene} = $intra_pi;
if ($na_if_missing_loci == 1 && $missing_loci > 0) {
$sample_gene_pi{$sample}{$gene} = "NA";
}
}
}
}
}
sub calc_per_gene_aminoacid_pi {
foreach $sample (@samples_plus) {
$tot_peptides = 0;
foreach $contig (@contigs) {
@genes = @{ $contig_genes{$contig} };
foreach $gene (@genes) {
$intra_pi = 0;
$missing_loci = 0;
#print"\n$gene\n";
foreach $locus (keys %{$gene_locus{$gene}}) {
$missing_loci = 1 if (!defined $sample_locus_pi{$sample}{$locus});
next if (!defined $sample_locus_pi{$sample}{$locus});
@fields = split(/\|/, $locus);
$contig = $fields[0];
$pos = $fields[1];
$tot_count = $sample_locus_totcount{$sample}{$locus};
@alleles = (keys %{$sample_locus_allel_counts{$sample}{$locus}});
#print"Alleles: @alleles\n";
for ($i = 0; $i < @alleles; $i++) {
$mod_contig_seq = $contig_seq{$contig};
substr($mod_contig_seq, ($pos-1), length($alleles[$i])) = $alleles[$i];
$mod_gene_seq = substr($mod_contig_seq, ($gene_start{$gene} - 1), $gene_length{$gene}); # OBS!!!
$mod_gene_seq = &make_revcomp($mod_gene_seq) if ($gene_strand{$gene} eq "-");
$peptide = "";
for ($j = 0; $j < $gene_length{$gene}; $j=$j+3) {
$codon = substr($mod_gene_seq, $j, 3);
$peptide = $peptide.$codon_aminoacid{$codon};
}
if (defined $sample_locus_gene_peptide_counts{$sample}{$locus}{$gene}{$peptide}) {
$sample_locus_gene_peptide_counts{$sample}{$locus}{$gene}{$peptide} = $sample_locus_gene_peptide_counts{$sample}{$locus}{$gene}{$peptide} + $sample_locus_allel_counts{$sample}{$locus}{$alleles[$i]};
} else {
$sample_locus_gene_peptide_counts{$sample}{$locus}{$gene}{$peptide} = $sample_locus_allel_counts{$sample}{$locus}{$alleles[$i]};
}
#print"\nLocus: $locus\nGene: $gene\nSample: $sample\nAllele: $alleles[$i]\nStrand: $gene_strand{$gene}\n>Gene_seq:\n$gene_seq{$gene}\n\n>Mod_seq:\n$mod_gene_seq\n\n>Mod_peptide:\n$peptide\n";
}
$locus_intra_pi = 0;
@peptides = (keys %{$sample_locus_gene_peptide_counts{$sample}{$locus}{$gene}});
for ($i = 0; $i < @peptides; $i++) {
#print"\nPeptide 1: $peptides[$i]\n";
$counts_1 = $sample_locus_gene_peptide_counts{$sample}{$locus}{$gene}{$peptides[$i]};
#print"Counts1: $counts_1\n";
$tot_peptides++ if ($counts_1 > 0);
for ($j = 0; $j < @peptides; $j++) {
next if ($peptides[$i] eq $peptides[$j]);
#print"Peptide 2: $peptides[$j]\n";
$counts_2 = $sample_locus_gene_peptide_counts{$sample}{$locus}{$gene}{$peptides[$j]};
#print"Counts2: $counts_2\n";
$locus_intra_pi = $locus_intra_pi + ($counts_1/$tot_count)*($counts_2/($tot_count - 1)); # According to Schloising
#$locus_intra_pi = $locus_intra_pi + ($counts_1/$tot_count)*($counts_2/($tot_count)); # According to our initial version
}
}
#print"Sample: $sample $locus locus_intra_pi: $locus_intra_pi\n";
$sample_locus_aminoacid_pi{$sample}{$locus} = $locus_intra_pi;
$intra_pi = $intra_pi + $locus_intra_pi;
#print"Sample: $sample $locus intra_pi: $intra_pi\n\n";
}
$intra_pi = $intra_pi/$gene_length{$gene};
$sample_gene_aminoacid_pi{$sample}{$gene} = $intra_pi;
#$sample_totpeptides{$sample} = $tot_peptides;
#print"Sample: $sample $locus intra_pi: $intra_pi\n\n";
if ($na_if_missing_loci == 1 && $missing_loci == 1) {
$sample_gene_aminoacid_pi{$sample}{$gene} = "NA";
}
}
}
}
}
sub calc_fst { # is it more logical to only include the loci where any inter-pi exist for the sample pair, and calculate mean fst for these loci?
print "Sample1\tSample2\tpi_1\tpi_2\tpi_1-2\tfst\n";
for ($ix1 = 0; $ix1 < @samples; $ix1++) {
$sample1 = $samples[$ix1];
#print"Sample1 $sample1\n";
for ($ix2 = $ix1 + 1; $ix2 < @samples; $ix2++) {
#for ($ix2 = $ix1 + 0; $ix2 < @samples; $ix2++) {
$sample2 = $samples[$ix2];
#print"Sample2 $sample2\n";
$inter_pi = 0;
$sample1_pi = $sample2_pi = 0; # intra-pi based on only loci shared by both samples
@loci = (keys %{$sample_locus_allel_counts{$sample1}});
#$temp = @loci;
#print"sample1: $sample1 num_loci: $temp\n"; die;
#print"sample1: $sample1 loci: @loci\n"; die;
foreach $locus (@loci) {
next if (!defined $sample_locus_allel_counts{$sample2}{$locus});
#print"Locus $locus\n";
@alleles1 = (keys %{$sample_locus_allel_counts{$sample1}{$locus}});
@alleles2 = (keys %{$sample_locus_allel_counts{$sample2}{$locus}});
$tot_count1 = $sample_locus_totcount{$sample1}{$locus};
$tot_count2 = $sample_locus_totcount{$sample2}{$locus};
#print"Alleles: @alleles1 @alleles2\n";
for ($i = 0; $i < @alleles1; $i++) {
#print"Allele 1: $alleles1[$i]\n";
$counts_1 = $sample_locus_allel_counts{$sample1}{$locus}{$alleles1[$i]};
#print"Counts1: $counts_1\n";
for ($j = 0; $j < @alleles2; $j++) {
next if ($alleles1[$i] eq $alleles2[$j]);
#print"Allele 2: $alleles2[$j]\n";
$counts_2 = $sample_locus_allel_counts{$sample2}{$locus}{$alleles2[$j]};
#print"Counts2: $counts_2\n";
$inter_pi = $inter_pi + ($counts_1/$tot_count1)*($counts_2/$tot_count2);
}
}
$sample1_pi = $sample1_pi + $sample_locus_pi{$sample1}{$locus};
$sample2_pi = $sample2_pi + $sample_locus_pi{$sample2}{$locus};
#$sample1_pi = $sample1_pi;
#$sample2_pi = $sample2_pi;
}
$inter_pi = $inter_pi/$genome_size;
$sample_sample_pi{$sample1}{$sample2} = $inter_pi;
$sample_sample_pi{$sample2}{$sample1} = $inter_pi;
$sample1_pi = $sample1_pi/$genome_size;
$sample2_pi = $sample2_pi/$genome_size;
if ($inter_pi > 0) {
#$fst = 1 - 0.5*($sample_pi{$sample1} + $sample_pi{$sample2})/$inter_pi; # intra pi values only based on all loci
$fst = 1 - 0.5*($sample1_pi + $sample2_pi)/$inter_pi # intra pi values only based on shared loci
} else {
$fst = "NA";
}
$fst = sprintf("%.4f", $fst);
$sample_sample_fst{$sample1}{$sample2} = $fst;
$sample_sample_fst{$sample2}{$sample1} = $fst;
print"$sample1\t$sample2\t$sample_pi{$sample1}\t$sample_pi{$sample2}\t$inter_pi\t$fst\n";
}
}
}
sub calc_per_gene_fst {
foreach $contig (@contigs) {
#print "Contig $contig\n";
@genes = @{ $contig_genes{$contig} };
foreach $gene (@genes) {
#print "Gene $gene\n";
@loci = (keys %{$gene_locus{$gene}});
next if (@loci == 0);
for ($ix1 = 0; $ix1 < @samples; $ix1++) {
$sample1 = $samples[$ix1];
#print"Sample1 $sample1\n";
for ($ix2 = $ix1 + 1; $ix2 < @samples; $ix2++) {
$sample2 = $samples[$ix2];
#print"Sample2 $sample2\n";
$inter_pi = 0;
$sample1_pi = $sample2_pi = 0;
foreach $locus (@loci) {
#print"Locus $locus\n";
next if (!defined $sample_locus_allel_counts{$sample1}{$locus});
next if (!defined $sample_locus_allel_counts{$sample2}{$locus});
@alleles1 = (keys %{$sample_locus_allel_counts{$sample1}{$locus}});
@alleles2 = (keys %{$sample_locus_allel_counts{$sample2}{$locus}});
$tot_count1 = $sample_locus_totcount{$sample1}{$locus};
$tot_count2 = $sample_locus_totcount{$sample2}{$locus};
#print"Alleles1: @alleles1 Alleles2: @alleles2\n";
for ($i = 0; $i < @alleles1; $i++) {
#print"Allele 1: $alleles1[$i]\n";
$counts_1 = $sample_locus_allel_counts{$sample1}{$locus}{$alleles1[$i]};
#print"Counts1: $counts_1\n";
for ($j = 0; $j < @alleles2; $j++) {
next if ($alleles1[$i] eq $alleles2[$j]);
#print"Allele 2: $alleles2[$j]\n";
$counts_2 = $sample_locus_allel_counts{$sample2}{$locus}{$alleles2[$j]};
#print"Counts2: $counts_2\n";
$inter_pi = $inter_pi + ($counts_1/$tot_count1)*($counts_2/$tot_count2);
#print"inter_pi $inter_pi\n";
}
}
$sample1_pi = $sample1_pi + $sample_locus_pi{$sample1}{$locus};
$sample2_pi = $sample2_pi + $sample_locus_pi{$sample2}{$locus};
}
$inter_pi = $inter_pi/$gene_length{$gene};
$sample_sample_gene_pi{$sample1}{$sample2}{$gene} = $inter_pi;
$sample_sample_gene_pi{$sample2}{$sample1}{$gene} = $inter_pi;
$sample1_pi = $sample1_pi/$gene_length{$gene};
$sample2_pi = $sample2_pi/$gene_length{$gene};
if ($inter_pi > 0) {
#$fst = 1 - 0.5*($sample_gene_pi{$sample1}{$gene} + $sample_gene_pi{$sample2}{$gene})/$inter_pi; # intra pi based on all loci
$fst = 1 - 0.5*($sample1_pi + $sample2_pi)/$inter_pi; # based on only shared loci
$fst = sprintf("%.4f", $fst);
} else {
$fst = "NA"; # i.e. no intra-pi in any of the two samples and consequently no inter-pi.
}
$sample_sample_gene_fst{$sample1}{$sample2}{$gene} = $fst;
$sample_sample_gene_fst{$sample2}{$sample1}{$gene} = $fst;
#print"$gene $sample1 $sample2 $sample_gene_pi{$sample1}{$gene} $sample_gene_pi{$sample2}{$gene} $inter_pi $fst\n";
}
}
}
}
}
# double check!
sub calc_per_gene_aminoacid_fst {
foreach $contig (@contigs) {
#print "Contig $contig\n";
@genes = @{ $contig_genes{$contig} };
foreach $gene (@genes) {
#print "Gene $gene\n";
@loci = (keys %{$gene_locus{$gene}});
next if (@loci == 0);
for ($ix1 = 0; $ix1 < @samples; $ix1++) {
$sample1 = $samples[$ix1];
#print"Sample1 $sample1\n";
for ($ix2 = $ix1 + 1; $ix2 < @samples; $ix2++) {
$sample2 = $samples[$ix2];
#print"Sample2 $sample2\n";
$inter_pi = 0;
$sample1_pi = $sample2_pi = 0;
foreach $locus (@loci) {
#print"\nLocus $locus\n";
next if (!defined $sample_locus_allel_counts{$sample1}{$locus});
next if (!defined $sample_locus_allel_counts{$sample2}{$locus});
@peptides1 = (keys %{$sample_locus_gene_peptide_counts{$sample1}{$locus}{$gene}});
@peptides2 = (keys %{$sample_locus_gene_peptide_counts{$sample2}{$locus}{$gene}});
$tot_count1 = $sample_locus_totcount{$sample1}{$locus};
$tot_count2 = $sample_locus_totcount{$sample2}{$locus};
#print"Peptides1: @peptides1 Peptides2: @peptides2\n";
for ($i = 0; $i < @peptides1; $i++) {
#print"Peptide 1: $peptides1[$i]\n";
$counts_1 = $sample_locus_gene_peptide_counts{$sample1}{$locus}{$gene}{$peptides1[$i]};
#print"Counts1: $counts_1\n";
for ($j = 0; $j < @peptides2; $j++) {
next if ($peptides1[$i] eq $peptides2[$j]);
#print"Peptide 2: $peptides2[$j]\n";
$counts_2 = $sample_locus_gene_peptide_counts{$sample2}{$locus}{$gene}{$peptides2[$j]};
#print"Counts2: $counts_2\n";
$inter_pi = $inter_pi + ($counts_1/$tot_count1)*($counts_2/$tot_count2);
}
}
$sample1_pi = $sample1_pi + $sample_locus_aminoacid_pi{$sample1}{$locus};
$sample2_pi = $sample2_pi + $sample_locus_aminoacid_pi{$sample2}{$locus};
}
$inter_pi = $inter_pi/$gene_length{$gene};
#print"$gene $sample1 $sample2 $inter_pi\n";
$sample_sample_gene_aminoacid_pi{$sample1}{$sample2}{$gene} = $inter_pi;
$sample_sample_gene_aminoacid_pi{$sample2}{$sample1}{$gene} = $inter_pi;
$sample1_pi = $sample1_pi/$gene_length{$gene};
$sample2_pi = $sample2_pi/$gene_length{$gene};
if ($inter_pi > 0) {
#$fst = 1 - 0.5*($sample_gene_aminoacid_pi{$sample1}{$gene} + $sample_gene_aminoacid_pi{$sample2}{$gene})/$inter_pi;
$fst = 1 - 0.5*($sample1_pi + $sample2_pi)/$inter_pi; # based on only shared loci
$fst = sprintf("%.4f", $fst);
} else {
$fst = "NA"; # i.e. no intra-pi in any of the two samples and consequently no inter-pi.
}
$sample_sample_gene_aminoacid_fst{$sample1}{$sample2}{$gene} = $fst;
$sample_sample_gene_aminoacid_fst{$sample2}{$sample1}{$gene} = $fst;
#print"$gene $sample1 $sample2 $sample1_pi $sample2_pi $inter_pi $fst\n"; # based on only shared loci
}
}
}
}
}
sub calc_pN_pS {
foreach $sample (@samples_plus) {
foreach $contig (@contigs) {
@genes = @{ $contig_genes{$contig} };
foreach $gene (@genes) {
$PN = 0; # non-synonomous polymorphisms