root/galaxy-central/tools/samtools/pileup_parser.pl @ 3

#! /usr/bin/perl -w

use strict;
use POSIX;


die "Usage: pileup_parser.pl <in_file> <ref_base_column> <read_bases_column> <base_quality_column> <coverage column> <qv cutoff> <coverage cutoff> <SNPs only?> <output bed?> <coord_column> <out_file> <total_diff> <print_qual_bases>\n" unless @ARGV == 13;

my $in_file = $ARGV[0];
my $ref_base_column = $ARGV[1]-1; # 1 based
my $read_bases_column = $ARGV[2]-1; # 1 based
my $base_quality_column = $ARGV[3]-1; # 1 based
my $cvrg_column = $ARGV[4]-1; # 1 based
my $quality_cutoff = $ARGV[5]; # phred scale integer
my $cvrg_cutoff = $ARGV[6]; # unsigned integer
my $SNPs_only = $ARGV[7]; # set to "Yes" to print only positions with SNPs; set to "No" to pring everything
my $bed = $ARGV[8]; #set to "Yes" to convert coordinates to bed format (0-based start, 1-based end); set to "No" to leave as is
my $coord_column = $ARGV[9]-1; #1 based 
my $out_file = $ARGV[10];
my $total_diff = $ARGV[11]; # set to "Yes" to print total number of deviant based
my $print_qual_bases = $ARGV[12]; #set to "Yes" to print quality and read base columns

my $invalid_line_counter = 0;
my $first_skipped_line = "";
my %SNPs = ('A',0,'T',0,'C',0,'G',0);
my $above_qv_bases = 0;
my $SNPs_exist = 0;
my $out_string = "";
my $diff_count = 0;

open (IN, "<$in_file") or die "Cannot open $in_file $!\n";
open (OUT, ">$out_file") or die "Cannot open $out_file $!\n";

while (<IN>) {
        chop;
        next if m/^\#/;
        my @fields = split /\t/;
        next if $fields[ $ref_base_column ] eq "*"; # skip indel lines
        my $read_bases   = $fields[ $read_bases_column ];
        die "Coverage column" . ($cvrg_column+1) . " contains non-numeric values. Check your input parameters as well as format of input dataset." if ( not isdigit $fields[ $cvrg_column ] );
    next if $fields[ $cvrg_column ] < $cvrg_cutoff;
        my $base_quality = $fields[ $base_quality_column ];
        if ($read_bases =~ m/[\$\^\+-]/) {
                $read_bases =~ s/\^.//g; #removing the start of the read segement mark
                $read_bases =~ s/\$//g; #removing end of the read segment mark
                while ($read_bases =~ m/[\+-]{1}(\d+)/g) {
                        my $indel_len = $1;
                        $read_bases =~ s/[\+-]{1}$indel_len.{$indel_len}//; # remove indel info from read base field
                }
        }
        if ( length($read_bases) != length($base_quality) ) {
        $first_skipped_line = $. if $first_skipped_line eq "";
        ++$invalid_line_counter;
        next;
        }
        # after removing read block and indel data the length of read_base 
        # field should identical to the length of base_quality field
        
        my @bases = split //, $read_bases;
        my @qv    = split //, $base_quality;
        
        for my $base ( 0 .. @bases - 1 ) {
                if ( ord( $qv[ $base ] ) - 33 >= $quality_cutoff and $bases[ $base ] ne '*')
                {
                        ++$above_qv_bases;
                        
                        if ( $bases[ $base ] =~ m/[ATGC]/i )
                        {
                                $SNPs_exist = 1;        
                                $SNPs{ uc( $bases[ $base ] ) } += 1;
                                $diff_count += 1;
                        } elsif ( $bases[ $base ] =~ m/[\.,]/ ) {
                            $SNPs{ uc( $fields[ $ref_base_column ] ) } += 1;
                    }                   
                }
        } 
        
        if ($bed eq "Yes") {
               my $start = $fields[ $coord_column ] - 1;
               my $end   = $fields[ $coord_column ];
               $fields[ $coord_column ] = "$start\t$end";
        } 
        
        if ($print_qual_bases ne "Yes") {
               $fields[ $base_quality_column ] = "";
               $fields[ $read_bases_column ] = "";
        }
               
        
        $out_string = join("\t", @fields); # \t$read_bases\t$base_quality";
        foreach my $SNP (sort keys %SNPs) {
                        $out_string .= "\t$SNPs{$SNP}";
        }
        
        if ($total_diff eq "Yes") {
           $out_string .= "\t$above_qv_bases\t$diff_count\n";
        } else {
           $out_string .= "\t$above_qv_bases\n";
        }       
        
        $out_string =~ s/\t+/\t/g;
        
        if ( $SNPs_only eq "Yes" ) {
                print OUT $out_string if $SNPs_exist == 1;
        } else {
                print OUT $out_string;
        }

                
        %SNPs = ();
        %SNPs = ('A',0,'T',0,'C',0,'G',0);
        $above_qv_bases = 0;
        $SNPs_exist = 0;
        $diff_count = 0;
        

}

print "Skipped $invalid_line_counter invalid line(s) beginning with line $first_skipped_line\n" if $invalid_line_counter > 0;
close IN;
close OUT;