#! /Users/runner/bioconda/conda-bld/gmap_1645506335088/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/perl

use warnings;
use IO::File;
use Getopt::Std;

undef($opt_c);			# desired_chr
$opt_w = 1;                     # item weight: 1 (more confident), 2, or 3 (less); allow $opt_w and lower
undef($opt_e);			# exceptions file (separate file provided for hg18 and earlier)
getopts("c:e:w:");


if (defined($exceptions_file = $opt_e)) {
    if ($exceptions_file =~ /\.gz$/) {
	$FP = new IO::File("gunzip -c $exceptions_file |") or die "Cannot gunzip file $exceptions_file";
    } else {
	$FP = new IO::File($exceptions_file) or die "Cannot read file $exceptions_file";
    }
    while (defined($line = <$FP>)) {
	$line =~ s/\r\n/\n/;
	chop $line;
	@fields = split /\t/,$line;
	$exception_type = $fields[5];

	if (!defined($allowp{$exception_type})) {
	    # Exclude this SNP (implicitly)
	    $rsid = $fields[4];
	    if (!defined($excludep{$rsid})) {
		$nexclude_implicit{$exception_type} += 1;
		$excludep{$rsid} = 1;
	    }
	    
	} elsif ($allowp{$exception_type} == 0) {
	    # Exclude this SNP (explicitly)
	    $rsid = $fields[4];
	    if (!defined($excludep{$rsid})) {
		$nexclude_explicit{$exception_type} += 1;
		$excludep{$rsid} = 1;
	    }

	} else {
	    # Allow this SNP
	    $nallow_explicit{$exception_type} += 1;
	}
    }
    close($FP);

    print STDERR "Exceptions to be allowed (allowp == 1 in dbsnp_iit program):\n";
    foreach $exception_type (sort {$a cmp $b} keys %nallow_explicit) {
	print STDERR "  $exception_type: $nallow_explicit{$exception_type}\n";
    }
    print STDERR "\n";
    
    print STDERR "Exceptions to be excluded (allowp == 0 in dbsnp_iit program):\n";
    foreach $exception_type (sort {$a cmp $b} (keys %nexclude_explicit)) {
	print STDERR "  $exception_type: $nexclude_explicit{$exception_type}\n";
    }
    print STDERR "\n";

    print STDERR "Exceptions excluded implicitly (not defined in allowp in dbsnp_iit program):\n";
    foreach $exception_type (sort {$a cmp $b} (keys %nexclude_implicit)) {
	print STDERR "  $exception_type: $nexclude_implicit{$exception_type}\n";
    }
    print STDERR "\n";

} else {
    print STDERR "Exceptions to be allowed (allowp == 1 in dbsnp_iit program):\n";
    foreach $exception_type (sort {$a cmp $b} keys %allowp) {
	if ($allowp{$exception_type} == 1) {
	    # Allow this SNP (explicitly)
	    print STDERR "  $exception_type\n";
	}
    }
    print STDERR "\n";

    print STDERR "Exceptions to be excluded (allowp == 0 in dbsnp_iit program):\n";
    foreach $exception_type (sort {$a cmp $b} keys %allowp) {
	if ($allowp{$exception_type} == 0) {
	    # Excluded this SNP (explicitly)
	    print STDERR "  $exception_type\n";
	}
    }
    print STDERR "\n";
}



while (defined($line = <>)) {
    $line =~ s/\r\n/\n/;
    chop $line;
    @fields = split /\t/,$line;
    $item_class = $fields[11];
    if ($item_class eq "single") {
	if (!defined($exceptions_file)) {
	    record_new_exceptions($fields[18]);
	}

	$chr = $fields[1];
	if (!defined($opt_c) || $chr eq $opt_c) {
	    $item_weight = $fields[17];
	    if ($item_weight <= $opt_w) {
		$rsid = $fields[4];
		if (defined($excludep{$rsid})) {
		    # Skip
		} elsif (defined($fields[18]) && exclude_for_exceptions($fields[18]) == 1) {
		    # Skip
		} elsif ($fields[9] =~ /^(.)\/(.)$/) {
		    # single base => single base
		    $alleleA = $1;
		    $alleleB = $2;
		    if (!defined($acgt{$alleleA}) || !defined($acgt{$alleleB})) {
			print STDERR "$rsid has alleles $fields[9] with non-ACGT character\n";
		    } else {
			if (($snp_strand = $fields[6]) eq "-") {
			    $alleleA = $revcomp{$alleleA};
			    $alleleB = $revcomp{$alleleB};
			}
			if ($alleleA le $alleleB) {
			    $snp_type = $alleleA . $alleleB;
			} else {
			    $snp_type = $alleleB . $alleleA;
			}
			$chrpos = $fields[2] + 1;	# because dbsnp file is 0-based
			print ">$rsid $chr:$chrpos $snp_type $snp_strand\n";
		    }
		}
	    }
	}
    }
}
    

if (!defined($exceptions_file)) {
    print STDERR "Exceptions excluded implicitly (not defined in allowp in dbsnp_iit program):\n";
    foreach $exception_type (sort {$a cmp $b} keys %newp) {
	print STDERR $exception_type . "\n";
    }
    print STDERR "\n";
}


exit;


sub record_new_exceptions {
    my ($exceptions) = @_;

    foreach $exception (split ",",$exceptions) {
	if (!defined($allowp{$exception})) {
	    $newp{$exception} = 1;
	}
    }
}



sub exclude_for_exceptions {
    my ($exceptions) = @_;

    foreach $exception (split ",",$exceptions) {
	if (!defined($allowp{$exception})) {
	    # Exclude this SNP (implicitly)
	    return 1;
	} elsif ($allowp{$exception} == 0) {
	    # Exclude this SNP (explicitly)
	    return 1;
	}
    }

    # Allow this SNP
    return 0;
}


BEGIN {
    %acgt = ("A" => 1, "C" => 1, "G" => 1, "T" => 1);

    %revcomp = ("A" => "T", "C" => "G", "G" => "C", "T" => "A");

    # To allow an exception type, it must be listed below and have a value of 1
    # These exceptions are taken from the *ExceptionDesc.txt file from UCSC

    %allowp = (
	"RefAlleleMismatch" => 0, # The reference allele from dbSNP does not match the UCSC reference allele.
	"RefAlleleRevComp" => 0,  # The reference allele from dbSNP matches the reverse complement of the UCSC reference allele.
	"DuplicateObserved" => 0, # There are other rsIds at this position with identical variation.
	"MixedObserved" => 0, #	There are other rsIds at this position with different variation.
	"FlankMismatchGenomeLonger" => 0, # NCBI's alignment of the flanking sequences had at least one mismatch or gap.  (UCSC's re-alignment of flanking sequences to the genome may be informative -- see below.)
	"FlankMismatchGenomeEqual" => 0, # NCBI's alignment of the flanking sequences had at least one mismatch or gap.  (UCSC's re-alignment of flanking sequences to the genome may be informative -- see below.)
	"FlankMismatchGenomeShorter" => 0, # NCBI's alignment of the flanking sequences had at least one mismatch or gap.  (UCSC's re-alignment of flanking sequences to the genome may be informative -- see below.)
	"NamedDeletionZeroSpan" => 0, # A deletion (from the genome) was observed but the annotation spans 0 bases.  (UCSC's re-alignment of flanking sequences to the genome may be informative -- see below.)
	"NamedInsertionNonzeroSpan" => 0, # An insertion (into the genome) was observed but the annotation spans more than 0 bases.  (UCSC's re-alignment of flanking sequences to the genome may be informative -- see below.)
	"SingleClassLongerSpan" => 0, # All observed alleles are single-base, but the annotation spans more than 1 base.  (UCSC's re-alignment of flanking sequences to the genome may be informative -- see below.)
	"SingleClassZeroSpan" => 0, # All observed alleles are single-base, but the annotation spans 0 bases.  (UCSC's re-alignment of flanking sequences to the genome may be informative -- see below.)
	"SingleClassTriAllelic" => 0, # This single-base substitution is tri-allelic.
	"SingleClassQuadAllelic" => 0, # This single-base substitution is quad-allelic.
	"ObservedWrongFormat" => 0, # Observed allele(s) from dbSNP have unexpected format for the given class.
	"ObservedTooLong" => 0, # Observed allele not given (length too long).
	"ObservedContainsIupac" => 0, # Observed allele(s) from dbSNP contain IUPAC ambiguous bases.
	"ObservedMismatch" => 0, # UCSC reference allele does not match any observed allele from dbSNP.
	"MultipleAlignments" => 0, # This variant aligns in more than one location.
	"NonIntegerChromCount" => 0, # At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed.  The reported total sample count for this SNP is probably incorrect.
	"AlleleFreqSumNot1" => 0, # Allele frequencies do not sum to 1.0 (+-0.010000).  This SNP's allele frequency data are probably incomplete.
	"InconsistentAlleles" => 0,
	"SingleAlleleFreq" => 0,
	);
}

