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122 lines
3.9 KiB
Perl
Executable File
122 lines
3.9 KiB
Perl
Executable File
#! /usr/bin/perl -w
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use strict;
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use POSIX;
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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;
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my $in_file = $ARGV[0];
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my $ref_base_column = $ARGV[1]-1; # 1 based
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my $read_bases_column = $ARGV[2]-1; # 1 based
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my $base_quality_column = $ARGV[3]-1; # 1 based
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my $cvrg_column = $ARGV[4]-1; # 1 based
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my $quality_cutoff = $ARGV[5]; # phred scale integer
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my $cvrg_cutoff = $ARGV[6]; # unsigned integer
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my $SNPs_only = $ARGV[7]; # set to "Yes" to print only positions with SNPs; set to "No" to pring everything
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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
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my $coord_column = $ARGV[9]-1; #1 based
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my $out_file = $ARGV[10];
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my $total_diff = $ARGV[11]; # set to "Yes" to print total number of deviant based
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my $print_qual_bases = $ARGV[12]; #set to "Yes" to print quality and read base columns
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my $invalid_line_counter = 0;
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my $first_skipped_line = "";
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my %SNPs = ('A',0,'T',0,'C',0,'G',0);
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my $above_qv_bases = 0;
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my $SNPs_exist = 0;
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my $out_string = "";
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my $diff_count = 0;
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open (IN, "<$in_file") or die "Cannot open $in_file $!\n";
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open (OUT, ">$out_file") or die "Cannot open $out_file $!\n";
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while (<IN>) {
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chop;
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next if m/^\#/;
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my @fields = split /\t/;
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next if $fields[ $ref_base_column ] eq "*"; # skip indel lines
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my $read_bases = $fields[ $read_bases_column ];
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die "Coverage column" . ($cvrg_column+1) . " contains non-numeric values. Check your input parameters as well as format of input dataset." if ( not isdigit $fields[ $cvrg_column ] );
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next if $fields[ $cvrg_column ] < $cvrg_cutoff;
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my $base_quality = $fields[ $base_quality_column ];
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if ($read_bases =~ m/[\$\^\+-]/) {
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$read_bases =~ s/\^.//g; #removing the start of the read segement mark
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$read_bases =~ s/\$//g; #removing end of the read segment mark
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while ($read_bases =~ m/[\+-]{1}(\d+)/g) {
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my $indel_len = $1;
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$read_bases =~ s/[\+-]{1}$indel_len.{$indel_len}//; # remove indel info from read base field
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}
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}
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if ( length($read_bases) != length($base_quality) ) {
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$first_skipped_line = $. if $first_skipped_line eq "";
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++$invalid_line_counter;
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next;
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}
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# after removing read block and indel data the length of read_base
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# field should identical to the length of base_quality field
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my @bases = split //, $read_bases;
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my @qv = split //, $base_quality;
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for my $base ( 0 .. @bases - 1 ) {
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if ( ord( $qv[ $base ] ) - 33 >= $quality_cutoff and $bases[ $base ] ne '*')
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{
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++$above_qv_bases;
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if ( $bases[ $base ] =~ m/[ATGC]/i )
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{
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$SNPs_exist = 1;
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$SNPs{ uc( $bases[ $base ] ) } += 1;
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$diff_count += 1;
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} elsif ( $bases[ $base ] =~ m/[\.,]/ ) {
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$SNPs{ uc( $fields[ $ref_base_column ] ) } += 1;
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}
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}
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}
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if ($bed eq "Yes") {
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my $start = $fields[ $coord_column ] - 1;
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my $end = $fields[ $coord_column ];
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$fields[ $coord_column ] = "$start\t$end";
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}
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if ($print_qual_bases ne "Yes") {
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$fields[ $base_quality_column ] = "";
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$fields[ $read_bases_column ] = "";
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}
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$out_string = join("\t", @fields); # \t$read_bases\t$base_quality";
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foreach my $SNP (sort keys %SNPs) {
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$out_string .= "\t$SNPs{$SNP}";
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}
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if ($total_diff eq "Yes") {
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$out_string .= "\t$above_qv_bases\t$diff_count\n";
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} else {
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$out_string .= "\t$above_qv_bases\n";
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}
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$out_string =~ s/\t+/\t/g;
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if ( $SNPs_only eq "Yes" ) {
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print OUT $out_string if $SNPs_exist == 1;
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} else {
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print OUT $out_string;
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}
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%SNPs = ();
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%SNPs = ('A',0,'T',0,'C',0,'G',0);
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$above_qv_bases = 0;
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$SNPs_exist = 0;
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$diff_count = 0;
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}
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print "Skipped $invalid_line_counter invalid line(s) beginning with line $first_skipped_line\n" if $invalid_line_counter > 0;
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close IN;
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close OUT;
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