95 lines
2.0 KiB
Perl
95 lines
2.0 KiB
Perl
package CIGAR;
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use strict;
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use warnings;
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use Nuc_translator;
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####
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sub construct_cigar {
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my ($genome_coords_aref, $query_coords_aref, $read_length, # required
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$genome_seq_sref, $strand # optional
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) = @_;
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my $cigar = "";
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for (my $i = 0; $i <= $#$genome_coords_aref; $i++) {
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my ($curr_genome_lend, $curr_genome_rend) = @{$genome_coords_aref->[$i]};
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my ($curr_query_lend, $curr_query_rend) = @{$query_coords_aref->[$i]};
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if ($i == 0) {
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if ($curr_query_lend > 1) {
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$cigar .= ($curr_query_lend - 1) . "S";
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}
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}
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else {
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my ($prev_genome_lend, $prev_genome_rend) = @{$genome_coords_aref->[$i-1]};
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my ($prev_query_lend, $prev_query_rend) = @{$query_coords_aref->[$i-1]};
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if ( (my $delta_genome = $curr_genome_lend - $prev_genome_rend) > 1) {
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my $deletion_intron_char = ($genome_seq_sref && $strand) ? &_check_intron_consensus($prev_genome_rend, $curr_genome_lend, $genome_seq_sref, $strand) : 'D'; # intron or deletion?
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$cigar .= ($delta_genome-1) . $deletion_intron_char;
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}
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if ( (my $delta_query = $curr_query_lend - $prev_query_rend) > 1) {
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$cigar .= ($delta_query-1) . "I";
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}
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}
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my $len = $curr_genome_rend - $curr_genome_lend + 1;
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$cigar .= "$len" . "M";
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if ($i == $#$genome_coords_aref) {
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if ($curr_query_rend < $read_length) {
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$cigar .= ($read_length - $curr_query_rend) . "S";
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}
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}
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}
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return($cigar);
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}
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####
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sub _check_intron_consensus {
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my ($left_segment_bound, $right_segment_bound, $genome_sref, $strand) = @_;
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my $left_dinuc = uc substr($$genome_sref, $left_segment_bound, 2);
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my $right_dinuc = uc substr($$genome_sref, $right_segment_bound-3, 2);
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if ($strand eq '-') {
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$left_dinuc = &reverse_complement($right_dinuc);
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$right_dinuc = &reverse_complement($left_dinuc);
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}
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if (
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( ($left_dinuc eq "GT" || $left_dinuc eq "GC") && $right_dinuc eq "AG")
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||
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($left_dinuc eq "CT" && $right_dinuc eq "AC")
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) {
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return("N"); # got splice pair
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}
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else {
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return("D"); # deletion
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}
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}
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1; #EOM
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