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galaxy/tools/regVariation/parseMAF_smallIndels.pl
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#!/usr/bin/perl -w
# a program to get indels
# input is a MAF format 3-way alignment file
# from 3-way blocks only at this time
# translate seq2, seq3, etc coordinates to + if align orient is reverse complement
use strict;
use warnings;
# declare and initialize variables
my $fh; # variable to store filehandle
my $record;
my $offset;
my $library = $ARGV[0];
my $count = 0;
my $count2 = 0;
my $count3 = 0;
my $count4 = 0;
my $start1 = my $start2 = my $start3 = my $start4 = my $start5 = my $start6 = 0;
my $orient = "";
my $outgroup = $ARGV[2];
my $ingroup1 = my $ingroup2 = "";
my $count_seq1insert = my $count_seq1delete = 0;
my $count_seq2insert = my $count_seq2delete = 0;
my $count_seq3insert = my $count_seq3delete = 0;
my @seq1_insert_lengths = my @seq1_delete_lengths = ();
my @seq2_insert_lengths = my @seq2_delete_lengths = ();
my @seq3_insert_lengths = my @seq3_delete_lengths = ();
my @seq1_insert = my @seq1_delete = my @seq2_insert = my @seq2_delete = my @seq3_insert = my @seq3_delete = ();
my @seq1_insert_startOnly = my @seq1_delete_startOnly = my @seq2_insert_startOnly = my @seq2_delete_startOnly = ();
my @seq3_insert_startOnly = my @seq3_delete_startOnly = ();
my @indels = ();
# check to make sure correct files
my $usage = "usage: parseMAF_smallIndels.pl [MAF.in] [small_Indels_summary.out] [outgroup]\n";
die $usage unless @ARGV == 3;
# perform some standard subroutines
$fh = open_file($library);
$offset = tell($fh);
#my $ofile = $ARGV[2];
#unless (open(OFILE, ">$ofile")){
# print "Cannot open output file \"$ofile\"\n\n";
# exit;
#}
my $ofile2 = $ARGV[1];
unless (open(OFILE2, ">$ofile2")){
print "Cannot open output file \"$ofile2\"\n\n";
exit;
}
# header line for output files
#print OFILE "# small indel events, parsed from MAF 3-way alignment file, coords are translated from (-) to (+) if necessary\n";
#print OFILE "#align\tingroup1\tingroup1_coord\tingroup1_orient\tingroup2\tingroup2_coord\tingroup2_orient\toutgroup\toutgroup_coord\toutgroup_orient\tindel_type\n";
#print OFILE2 "# small indels summary, parsed from MAF 3-way alignment file, coords are translated from (-) to (+) if necessary\n";
print OFILE2 "#block\tindel_type\tindel_length\tingroup1\tingroup1_start\tingroup1_end\tingroup1_alignSize\tingroup1_orient\tingroup2\tingroup2_start\tingroup2_end\tingroup2_alignSize\tingroup2_orient\toutgroup\toutgroup_start\toutgroup_end\toutgroup_alignSize\toutgroup_orient\n";
# main body of program
while ($record = get_next_record($fh) ){
if ($record=~ m/\s*##maf(.*)\s*# maf/s){
next;
}
my @sequences = get_sequences_within_block($record);
my @seq_info = get_indels_within_block(@sequences);
get_indels_lengths(@seq_info);
$offset = tell($fh);
$count++;
}
get_starts_only(@seq1_insert);
get_starts_only(@seq1_delete);
get_starts_only(@seq2_insert);
get_starts_only(@seq2_delete);
get_starts_only(@seq3_insert);
get_starts_only(@seq3_delete);
# print some things to keep track of progress
#print "# $library\n";
#print "# number of records = $count\n";
#print "# number of sequence \"s\" lines = $count2\n";
if ($count3 != 0){
print "Skipped $count3 blocks with only 2 seqs;\n";
}
#print "# number of records with only h-m = $count4\n\n";
print "Ingroup1 = $ingroup1; Ingroup2 = $ingroup2; Outgroup = $outgroup;\n";
print "# of ingroup1 inserts = $count_seq1insert;\n";
print "# of ingroup1 deletes = $count_seq1delete;\n";
print "# of ingroup2 inserts = $count_seq2insert;\n";
print "# of ingroup2 deletes = $count_seq2delete;\n";
print "# of outgroup3 inserts = $count_seq3insert;\n";
print "# of outgroup3 deletes = $count_seq3delete\n";
#close OFILE;
if ($count == $count3){
print STDERR "Skipped all blocks since none of them contain 3-way alignments.\n";
exit -1;
}
###################SUBROUTINES#####################################
# subroutine to open file
sub open_file {
my($filename) = @_;
my $fh;
unless (open($fh, $filename)){
print "Cannot open file $filename\n";
exit;
}
return $fh;
}
# get next record
sub get_next_record {
my ($fh) = @_;
my ($offset);
my ($record) = "";
my ($save_input_separator) = $/;
$/ = "a score";
$record = <$fh>;
$/ = $save_input_separator;
return $record;
}
# get header info
sub get_sequences_within_block{
my (@alignment) = @_;
my @lines = ();
my @sequences = ();
@lines = split ("\n", $record);
foreach (@lines){
chomp($_);
if (m/^\s*$/){
next;
}
elsif (m/^\s*=(\d+\.*\d*)/){
}elsif (m/^\s*s(.*)$/){
$count2++;
push (@sequences,$_);
}
}
return @sequences;
}
sub get_indels_within_block{
my (@sequences) = @_;
my $line1 = my $line2 = my $line3 = "";
my @line1 = my @line2 = my @line3 = ();
my $score = 0;
my $start1 = my $align_length1 = my $end1 = my $seq_length1 = 0;
my $start2 = my $align_length2 = my $end2 = my $seq_length2 = 0;
my $start3 = my $align_length3 = my $end3 = my $seq_length3 = 0;
my $seq1 = my $orient1 = "";
my $seq2 = my $orient2 = "";
my $seq3 = my $orient3 = "";
my $start1_plus = my $end1_plus = 0;
my $start2_plus = my $end2_plus = 0;
my $start3_plus = my $end3_plus = 0;
my @test = ();
my $test = "";
my $header = "";
my @header = ();
my $sequence1 = my $sequence2 = my $sequence3 ="";
my @array_return = ();
my $test1 = 0;
my $line1_stat = my $line2_stat = my $line3_stat = "";
# process 3-way blocks only
if (scalar(@sequences) == 3){
$line1 = $sequences[0];
chomp ($line1);
$line2 = $sequences[1];
chomp ($line2);
$line3 = $sequences[2];
chomp ($line3);
# check order of sequences and assign uniformly seq1= human, seq2 = chimp, seq3 = macaque
if ($line1 =~ m/$outgroup/){
$line1_stat = "out";
$line2=~ s/^\s*//;
$line2 =~ s/\s+/\t/g;
@line2 = split(/\t/, $line2);
if (($ingroup1 eq "") || ($line2[1] =~ m/$ingroup1/)){
$line2_stat = "in1";
$line3_stat = "in2";
}
else{
$line3_stat = "in1";
$line2_stat = "in2"; }
}
elsif ($line2 =~ m/$outgroup/){
$line2_stat = "out";
$line1=~ s/^\s*//;
$line1 =~ s/\s+/\t/g;
@line1 = split(/\t/, $line1);
if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){
$line1_stat = "in1";
$line3_stat = "in2";
}
else{
$line3_stat = "in1";
$line1_stat = "in2"; }
}
elsif ($line3 =~ m/$outgroup/){
$line3_stat = "out";
$line1=~ s/^\s*//;
$line1 =~ s/\s+/\t/g;
@line1 = split(/\t/, $line1);
if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){
$line1_stat = "in1";
$line2_stat = "in2";
}
else{
$line2_stat = "in1";
$line1_stat = "in2"; }
}
#print "# l1 = $line1_stat\n";
#print "# l2 = $line2_stat\n";
#print "# l3 = $line3_stat\n";
my $linei1 = my $linei2 = my $lineo = "";
my @linei1 = my @linei2 = my @lineo = ();
if ($line1_stat eq "out"){
$lineo = $line1;
}
elsif ($line1_stat eq "in1"){
$linei1 = $line1;
}
else{
$linei2 = $line1;
}
if ($line2_stat eq "out"){
$lineo = $line2;
}
elsif ($line2_stat eq "in1"){
$linei1 = $line2;
}
else{
$linei2 = $line2;
}
if ($line3_stat eq "out"){
$lineo = $line3;
}
elsif ($line3_stat eq "in1"){
$linei1 = $line3;
}
else{
$linei2 = $line3;
}
$linei1=~ s/^\s*//;
$linei1 =~ s/\s+/\t/g;
@linei1 = split(/\t/, $linei1);
$end1 =($linei1[2]+$linei1[3]-1);
$seq1 = $linei1[1].":".$linei1[3];
$ingroup1 = (split(/\./, $seq1))[0];
$start1 = $linei1[2];
$align_length1 = $linei1[3];
$orient1 = $linei1[4];
$seq_length1 = $linei1[5];
$sequence1 = $linei1[6];
$test1 = length($sequence1);
my $total_length1 = $test1+$start1;
my @array1 = ($start1,$end1,$orient1,$seq_length1);
($start1_plus, $end1_plus) = convert_coords(@array1);
$linei2=~ s/^\s*//;
$linei2 =~ s/\s+/\t/g;
@linei2 = split(/\t/, $linei2);
$end2 =($linei2[2]+$linei2[3]-1);
$seq2 = $linei2[1].":".$linei2[3];
$ingroup2 = (split(/\./, $seq2))[0];
$start2 = $linei2[2];
$align_length2 = $linei2[3];
$orient2 = $linei2[4];
$seq_length2 = $linei2[5];
$sequence2 = $linei2[6];
my $test2 = length($sequence2);
my $total_length2 = $test2+$start2;
my @array2 = ($start2,$end2,$orient2,$seq_length2);
($start2_plus, $end2_plus) = convert_coords(@array2);
$lineo=~ s/^\s*//;
$lineo =~ s/\s+/\t/g;
@lineo = split(/\t/, $lineo);
$end3 =($lineo[2]+$lineo[3]-1);
$seq3 = $lineo[1].":".$lineo[3];
$start3 = $lineo[2];
$align_length3 = $lineo[3];
$orient3 = $lineo[4];
$seq_length3 = $lineo[5];
$sequence3 = $lineo[6];
my $test3 = length($sequence3);
my $total_length3 = $test3+$start3;
my @array3 = ($start3,$end3,$orient3,$seq_length3);
($start3_plus, $end3_plus) = convert_coords(@array3);
#print "# l1 = $ingroup1\n";
#print "# l2 = $ingroup2\n";
#print "# l3 = $outgroup\n";
my $ABC = "";
my $coord1 = my $coord2 = my $coord3 = 0;
$coord1 = $start1_plus;
$coord2 = $start2_plus;
$coord3 = $start3_plus;
for (my $position = 0; $position < $test1; $position++) {
my $indelType = "";
my $indel_line = "";
# seq1 deletes
if ((substr($sequence1,$position,1) eq "-")
&& (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/)
&& (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){
$ABC = join("",($ABC,"X"));
my @s = split(/:/, $seq1);
$indelType = $s[0]."_delete";
#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
push (@indels,$indel_line);
push (@seq1_delete,$indel_line);
$coord2++; $coord3++;
}
# seq2 deletes
elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/)
&& (substr($sequence2,$position,1) eq "-")
&& (substr($sequence3,$position,1) !~ m/[-*\$?^]/)){
$ABC = join("",($ABC,"Y"));
my @s = split(/:/, $seq2);
$indelType = $s[0]."_delete";
#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
push (@indels,$indel_line);
push (@seq2_delete,$indel_line);
$coord1++;
$coord3++;
}
# seq1 inserts
elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/)
&& (substr($sequence2,$position,1) eq "-")
&& (substr($sequence3,$position,1) eq "-")){
$ABC = join("",($ABC,"Z"));
my @s = split(/:/, $seq1);
$indelType = $s[0]."_insert";
#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
push (@indels,$indel_line);
push (@seq1_insert,$indel_line);
$coord1++;
}
# seq2 inserts
elsif ((substr($sequence1,$position,1) eq "-")
&& (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/)
&& (substr($sequence3,$position,1) eq "-")){
$ABC = join("",($ABC,"W"));
my @s = split(/:/, $seq2);
$indelType = $s[0]."_insert";
#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
push (@indels,$indel_line);
push (@seq2_insert,$indel_line);
$coord2++;
}
# seq3 deletes
elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/)
&& (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/)
&& (substr($sequence3,$position,1) eq "-")){
$ABC = join("",($ABC,"S"));
my @s = split(/:/, $seq3);
$indelType = $s[0]."_delete";
#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
push (@indels,$indel_line);
push (@seq3_delete,$indel_line);
$coord1++; $coord2++;
}
# seq3 inserts
elsif ((substr($sequence1,$position,1) eq "-")
&& (substr($sequence2,$position,1) eq "-")
&& (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){
$ABC = join("",($ABC,"T"));
my @s = split(/:/, $seq3);
$indelType = $s[0]."_insert";
#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
push (@indels,$indel_line);
push (@seq3_insert,$indel_line);
$coord3++;
}else{
$ABC = join("",($ABC,"N"));
$coord1++; $coord2++; $coord3++;
}
}
@array_return=($seq1,$seq2,$seq3,$ABC);
return (@array_return);
}
# ignore pairwise cases for now, just count the number of blocks
elsif (scalar(@sequences) == 2){
my $ABC = "";
my $coord1 = my $coord2 = my $coord3 = 0;
$count3++;
$line1 = $sequences[0];
$line2 = $sequences[1];
chomp ($line1);
chomp ($line2);
if ($line2 !~ m/$ingroup2/){
$count4++;
}
}
}
sub get_indels_lengths{
my (@array) = @_;
if (scalar(@array) == 4){
my $seq1 = $array[0]; my $seq2 = $array[1]; my $seq3 = $array[2]; my $ABC = $array[3];
while ($ABC =~ m/(X+)/g) {
push (@seq1_delete_lengths,length($1));
$count_seq1delete++;
}
while ($ABC =~ m/(Y+)/g) {
push (@seq2_delete_lengths,length($1));
$count_seq2delete++;
}
while ($ABC =~ m/(S+)/g) {
push (@seq3_delete_lengths,length($1));
$count_seq3delete++;
}
while ($ABC =~ m/(Z+)/g) {
push (@seq1_insert_lengths,length($1));
$count_seq1insert++;
}
while ($ABC =~ m/(W+)/g) {
push(@seq2_insert_lengths,length($1));
$count_seq2insert++;
}
while ($ABC =~ m/(T+)/g) {
push (@seq3_insert_lengths,length($1));
$count_seq3insert++;
}
}
elsif (scalar(@array) == 0){
next;
}
}
# convert to coordinates to + strand if align orient = -
sub convert_coords{
my (@array) = @_;
my $s = $array[0];
my $e = $array[1];
my $o = $array[2];
my $l = $array[3];
my $start_plus = my $end_plus = 0;
if ($o eq "-"){
$start_plus = ($l - $e);
$end_plus = ($l - $s);
}elsif ($o eq "+"){
$start_plus = $s;
$end_plus = $e;
}
return ($start_plus, $end_plus);
}
# get first line only for each event
sub get_starts_only{
my (@test) = @_;
my $seq1 = my $seq2 = my $seq3 = my $indelType = my $old_seq1 = my $old_seq2 = my $old_seq3 = my $old_indelType = my $old_line = "";
my $coord1 = my $coord2 = my $coord3 = my $old_coord1 = my $old_coord2 = my $old_coord3 = 0;
my @matches = ();
my @seq1_insert = my @seq1_delete = my @seq2_insert = my @seq2_delete = my @seq3_insert = my @seq3_delete = ();
foreach my $line (@test){
chomp($line);
$line =~ s/^\s*//;
$line =~ s/\s+/\t/g;
my @line1 = split(/\t/, $line);
$seq1 = $line1[1];
$coord1 = $line1[2];
$seq2 = $line1[4];
$coord2 = $line1[5];
$seq3 = $line1[7];
$coord3 = $line1[8];
$indelType = $line1[10];
if ($indelType =~ m/$ingroup1/ && $indelType =~ m/insert/){
if ($coord1 != $old_coord1+1 || ($coord2 != $old_coord2 || $coord3 != $old_coord3)){
$start1++;
push (@seq1_insert_startOnly,$line);
}
}
elsif ($indelType =~ m/$ingroup1/ && $indelType =~ m/delete/){
if ($coord1 != $old_coord1 || ($coord2 != $old_coord2+1 || $coord3 != $old_coord3+1)){
$start2++;
push(@seq1_delete_startOnly,$line);
}
}
elsif ($indelType =~ m/$ingroup2/ && $indelType =~ m/insert/){
if ($coord2 != $old_coord2+1 || ($coord1 != $old_coord1 || $coord3 != $old_coord3)){
$start3++;
push(@seq2_insert_startOnly,$line);
}
}
elsif ($indelType =~ m/$ingroup2/ && $indelType =~ m/delete/){
if ($coord2 != $old_coord2 || ($coord1 != $old_coord1+1 || $coord3 != $old_coord3+1)){
$start4++;
push(@seq2_delete_startOnly,$line);
}
}
elsif ($indelType =~ m/$outgroup/ && $indelType =~ m/insert/){
if ($coord3 != $old_coord3+1 || ($coord1 != $old_coord1 || $coord2 != $old_coord2)){
$start5++;
push(@seq3_insert_startOnly,$line);
}
}
elsif ($indelType =~ m/$outgroup/ && $indelType =~ m/delete/){
if ($coord3 != $old_coord3 || ($coord1 != $old_coord1+1 ||$coord2 != $old_coord2+1)){
$start6++;
push(@seq3_delete_startOnly,$line);
}
}
$old_indelType = $indelType;
$old_seq1 = $seq1;
$old_coord1 = $coord1;
$old_seq2 = $seq2;
$old_coord2 = $coord2;
$old_seq3 = $seq3;
$old_coord3 = $coord3;
$old_line = $line;
}
}
# append lengths to each event start line
my $counter1; my $counter2; my $counter3; my $counter4; my $counter5; my $counter6;
my @final1 = my @final2 = my @final3 = my @final4 = my @final5 = my @final6 = ();
my $final_line1 = my $final_line2 = my $final_line3 = my $final_line4 = my $final_line5 = my $final_line6 = "";
for ($counter1 = 0; $counter1 < @seq3_insert_startOnly; $counter1++){
$final_line1 = join("\t",($seq3_insert_startOnly[$counter1],$seq3_insert_lengths[$counter1]));
push (@final1,$final_line1);
}
for ($counter2 = 0; $counter2 < @seq3_delete_startOnly; $counter2++){
$final_line2 = join("\t",($seq3_delete_startOnly[$counter2],$seq3_delete_lengths[$counter2]));
push(@final2,$final_line2);
}
for ($counter3 = 0; $counter3 < @seq2_insert_startOnly; $counter3++){
$final_line3 = join("\t",($seq2_insert_startOnly[$counter3],$seq2_insert_lengths[$counter3]));
push(@final3,$final_line3);
}
for ($counter4 = 0; $counter4 < @seq2_delete_startOnly; $counter4++){
$final_line4 = join("\t",($seq2_delete_startOnly[$counter4],$seq2_delete_lengths[$counter4]));
push(@final4,$final_line4);
}
for ($counter5 = 0; $counter5 < @seq1_insert_startOnly; $counter5++){
$final_line5 = join("\t",($seq1_insert_startOnly[$counter5],$seq1_insert_lengths[$counter5]));
push(@final5,$final_line5);
}
for ($counter6 = 0; $counter6 < @seq1_delete_startOnly; $counter6++){
$final_line6 = join("\t",($seq1_delete_startOnly[$counter6],$seq1_delete_lengths[$counter6]));
push(@final6,$final_line6);
}
# format final output
# # if inserts, increase coords for the sequence inserted, other sequences give coords for 5' and 3' bases flanking the gap
# # for deletes, increase coords for other 2 sequences and the one deleted give coords for 5' and 3' bases flanking the gap
get_final_format(@final5);
get_final_format(@final6);
get_final_format(@final3);
get_final_format(@final4);
get_final_format(@final1);
get_final_format(@final2);
sub get_final_format{
my (@final) = @_;
foreach (@final){
my $event_line = $_;
my @events = split(/\t/, $event_line);
my $event_type = $events[10];
my @name_align1 = split(/:/, $events[1]);
my @name_align2 = split(/:/, $events[4]);
my @name_align3 = split(/:/, $events[7]);
my $seq1_event_start = my $seq1_event_end = my $seq2_event_start = my $seq2_event_end = my $seq3_event_start = my $seq3_event_end = 0;
my $final_event_line = "";
# seq1_insert
if ($event_type =~ m/$ingroup1/ && $event_type =~ m/insert/){
# only increase coord for human
# remember that other two sequnences, the gap spans (coord - 1) --> coord
$seq1_event_start = ($events[2]);
$seq1_event_end = ($events[2]+$events[11]-1);
$seq2_event_start = ($events[5]-1);
$seq2_event_end = ($events[5]);
$seq3_event_start = ($events[8]-1);
$seq3_event_end = ($events[8]);
$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
}
# seq1_delete
elsif ($event_type =~ m/$ingroup1/ && $event_type =~ m/delete/){
# only increase coords for seq2 and seq3
# remember for seq1, the gap spans (coord - 1) --> coord
$seq1_event_start = ($events[2]-1);
$seq1_event_end = ($events[2]);
$seq2_event_start = ($events[5]);
$seq2_event_end = ($events[5]+$events[11]-1);
$seq3_event_start = ($events[8]);
$seq3_event_end = ($events[8]+$events[11]-1);
$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
}
# seq2_insert
elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/insert/){
# only increase coords for seq2
# remember that other two sequnences, the gap spans (coord - 1) --> coord
$seq1_event_start = ($events[2]-1);
$seq1_event_end = ($events[2]);
$seq2_event_start = ($events[5]);
$seq2_event_end = ($events[5]+$events[11]-1);
$seq3_event_start = ($events[8]-1);
$seq3_event_end = ($events[8]);
$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
}
# seq2_delete
elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/delete/){
# only increase coords for seq1 and seq3
# remember for seq2, the gap spans (coord - 1) --> coord
$seq1_event_start = ($events[2]);
$seq1_event_end = ($events[2]+$events[11]-1);
$seq2_event_start = ($events[5]-1);
$seq2_event_end = ($events[5]);
$seq3_event_start = ($events[8]);
$seq3_event_end = ($events[8]+$events[11]-1);
$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
}
# start testing w/seq3_insert
elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/insert/){
# only increase coord for rheMac
# remember that other two sequnences, the gap spans (coord - 1) --> coord
$seq1_event_start = ($events[2]-1);
$seq1_event_end = ($events[2]);
$seq2_event_start = ($events[5]-1);
$seq2_event_end = ($events[5]);
$seq3_event_start = ($events[8]);
$seq3_event_end = ($events[8]+$events[11]-1);
$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
}
# seq3_delete
elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/delete/){
# only increase coords for seq1 and seq2
# remember for seq3, the gap spans (coord - 1) --> coord
$seq1_event_start = ($events[2]);
$seq1_event_end = ($events[2]+$events[11]-1);
$seq2_event_start = ($events[5]);
$seq2_event_end = ($events[5]+$events[11]-1);
$seq3_event_start = ($events[8]-1);
$seq3_event_end = ($events[8]);
$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
}
print OFILE2 "$final_event_line\n";
}
}
close OFILE2;
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