/tools/samtools/pileup_parser.pl
https://bitbucket.org/cistrome/cistrome-harvard/ · Perl · 121 lines · 96 code · 22 blank · 3 comment · 23 complexity · 25b7d668adc30a5b81f7aa2596b92c75 MD5 · raw file
- #! /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;