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score_bisulfite_SNPs.pl
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sub score_bisulfite_SNPs{
my ($line,$chr,$genomic_pos,$read_base,$genome1,$genome2,$irrelevant) = @_;
my $first_read_conversion;
my $genome_conversion;
# warn "$line\n"; sleep(1);
my $strand;
while ( $line =~ /(XR|XG):Z:([^\t]+)/g ) {
my $tag = $1;
my $value = $2;
chomp $value;
if ($tag eq "XR") {
$first_read_conversion = $value;
$first_read_conversion =~ s/\r//;
}
elsif ($tag eq "XG") {
$genome_conversion = $value;
$genome_conversion =~ s/\r//;
}
}
if ($first_read_conversion eq 'CT' and $genome_conversion eq 'CT') {
$strand = 'OT'; ## this is OT
}
elsif ($first_read_conversion eq 'GA' and $genome_conversion eq 'CT') {
$strand = 'CTOT'; ## this is CTOT
}
elsif ($first_read_conversion eq 'GA' and $genome_conversion eq 'GA') {
$strand = 'CTOB'; ## this is CTOB
}
elsif ($first_read_conversion eq 'CT' and $genome_conversion eq 'GA') {
$strand = 'OB'; ## this is OB
}
else {
die "Unexpected combination of read and genome conversion: $first_read_conversion / $genome_conversion\n";
}
### if the SNP in question involves a genomic C position we potentially need to allow both C or T as C (G/A for the reverse strand)
if ( $snps{$chr}->{$genomic_pos}->{ref} eq 'C'){ # the position is a C in the reference genome
### C>T SNP. Can't use the position for top strand alignments
if ($snps{$chr}->{$genomic_pos}->{snp} eq 'T'){
if ($strand eq 'OT' or $strand eq 'CTOT'){
if ($verbose){ warn "This is a C>T SNP and can't be considered for OT or CTOT alignments!\n";}
++$ct_snp;
return ($genome1,$genome2,$irrelevant);
}
elsif ($strand eq 'OB' or $strand eq 'CTOB'){
if ($read_base eq 'C'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'T'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'G'){
if ($strand eq 'OT' or $strand eq 'CTOT'){
if ($read_base eq 'C' or $read_base eq 'T'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'G'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
elsif ($strand eq 'OB' or $strand eq 'CTOB'){
if ($read_base eq 'C'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'G' or $read_base eq 'A'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'A'){
if ($strand eq 'OT' or $strand eq 'CTOT'){
if ($read_base eq 'C' or $read_base eq 'T'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'A'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
elsif ($strand eq 'OB' or $strand eq 'CTOB'){
if ($read_base eq 'C'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'A'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'C') {
die "The ref is the same as snp, which should not happen in snpfile.\n"
}
}
if ( $snps{$chr}->{$genomic_pos}->{ref} eq 'A'){
if ($snps{$chr}->{$genomic_pos}->{snp} eq 'G'){
if ($strand eq 'OB' or $strand eq 'CTOB'){
if ($verbose){ warn "This is a A>G SNP and can't be considered for OB or CTOB alignments!\n";}
++$ct_snp;
return ($genome1,$genome2,$irrelevant);
}
elsif ($strand eq 'OT' or $strand eq 'CTOT'){
if ($read_base eq 'A'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'G'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'C'){
if ($strand eq 'OT' or $strand eq 'CTOT'){
if ($read_base eq 'A'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'C' or $read_base eq 'T'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
elsif ($strand eq 'OB' or $strand eq 'CTOB'){
if ($read_base eq 'A'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'C'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'T'){
if ($read_base eq 'A'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'T'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'A') {
die "The ref is the same as snp, which should not happen in snpfile.\n"
}
}
if ( $snps{$chr}->{$genomic_pos}->{ref} eq 'T'){
if ($snps{$chr}->{$genomic_pos}->{snp} eq 'C'){
if ($strand eq 'OT' or $strand eq 'CTOT'){
if ($verbose){ warn "This is a T>C SNP and can't be considered for OT or CTOT alignments!\n";}
++$ct_snp;
return ($genome1,$genome2,$irrelevant);
}
elsif ($strand eq 'OB' or $strand eq 'CTOB'){
if ($read_base eq 'T'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'C'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'G'){
if ($strand eq 'OT' or $strand eq 'CTOT'){
if ($read_base eq 'T'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'G'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
elsif ($strand eq 'OB' or $strand eq 'CTOB'){
if ($read_base eq 'T'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'G' or $read_base eq 'A'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'A'){
if ($read_base eq 'T'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'A'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'T') {
die "The ref is the same as snp, which should not happen in snpfile.\n"
}
}
if ( $snps{$chr}->{$genomic_pos}->{ref} eq 'G'){
if ($snps{$chr}->{$genomic_pos}->{snp} eq 'A'){
if ($strand eq 'OB' or $strand eq 'CTOB'){
if ($verbose){ warn "This is a G>A SNP and can't be considered for OB or CTOB alignments!\n";}
++$ct_snp;
return ($genome1,$genome2,$irrelevant);
}
elsif ($strand eq 'OT' or $strand eq 'CTOT'){
if ($read_base eq 'G'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'T'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'T'){
if ($strand eq 'OT' or $strand eq 'CTOT'){
if ($read_base eq 'G'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'T'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
elsif ($strand eq 'OB' or $strand eq 'CTOB'){
if ($read_base eq 'G' or $read_base eq 'A'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'T'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'C'){
if ($strand eq 'OT' or $strand eq 'CTOT'){
if ($read_base eq 'C' or $read_base eq 'T'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
elsif ($read_base eq 'G'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
elsif ($strand eq 'OB' or $strand eq 'CTOB'){
if ($read_base eq 'G' or $read_base eq 'A'){
if ($verbose){ warn "genome 1 specific!\n";}
++$genome1;
}
elsif ($read_base eq 'C'){
if ($verbose){ warn "genome 2 specific!\n";}
++$genome2;
}
else{
if ($verbose){ warn "The base was different than both genome 1 or genome 2: $read_base\n";}
++$irrelevant;
}
}
else{
die "Unable to identify read alignment strand\n";
}
}
elsif ($snps{$chr}->{$genomic_pos}->{snp} eq 'G') {
die "The ref is the same as snp, which should not happen in snpfile.\n"
}
}
return ($genome1,$genome2,$irrelevant);
}