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DealGeneWise.pl
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#!/usr/local/bin/perl
my $Author = "Hongkun Zheng";
my $Date = "2004-4-22";
my $Function= "Deal with GeneWise result to get gene paralog families!";
my $Contact = "zhenghk\@genomics.org.cn";
my $Version = "V.1.0";
my $Version = "V.2.0";
my $Update = "2004-4-22 11:21";
my $modify = "Modify the genomic position when happens frameshift!";
my $Version = "V.2.2";
my $Update = "2004-8-21 13:51";
my $Version = "V.3.0";
my $Update = "2004-10-26 13:32";
my $modify = "debug the exon number when frameshift happen.";
my $Version = "V.4.0";
my $Update = "2004-11-5 14:21";
my $modify = "use gap instead the codon in different exons, or exons is not start with phase 0!";
my $Version = "V.4.2";
my $Update = "2004-11-12 14:02";
my $modify = "add gap instead of intron like indels.";
my $Version = "V.4.4";
my $Version = "V.5.0";
my $Update = "2004-11-16 14:58";
my $modify = "Modify identity calculation to ignore gap.";
my $Version = "V.5.2";
my $Update = "2004-11-17 11:28";
my $modify = "Add the true codon in different exons.";
my $Version = "V.6.0";
my $Update = "2004-11-18 0:08:14";
my $modify = "debug Multiple sequence generation, correct the InDel position.";
my $Version = "V.6.2";
my $Update = "2004-11-19 21:39";
my $modify = "debug split codon count.";
my $Version = "V.6.4";
my $modify = "debug before start indels.";
my $Version = "V.6.6";
my $Update = "2005-3-16";
my $modify = "debug, added split codon position.";
my $modify = "debug, add unsupport protion region.";
my $Update = "2005-3-17";
my $modify = "debug, deal with frameshift in sub function CountExon();";
my $modify = "add BLAT like output file.";
my $Version = "V.7.0";
my $Update = "2005-3-21 15:51";
my $modify = "frameshift porblems;";
my $Version = "V.8.0";
my $Update = "2005-3-22 18:56";
my $modify = "change the arithmetic of the exon length;";
my $Version = "V.8.2";
my $Update = "2005-7-31 11:43";
my $modify = "add the sort part within the program.";
my $Version = "V.8.4";
my $Update = "2006-02-14 14:08";
my $modify = "debug NULL dna_name.";
my $modify = "revised input and output options.";
my $Version = "V.8.6";
my $Update = "2006-02-14 15:16";
my $modify = "change the method to sort genewise input file.";
my $Update = "2006-05-18 09:18";
my $modify = "debug, when the space is at the end of the line, the reverse the seq and remove it first.";
my $Update = "2005-05-22 15:55";
my $modify = "reverse space string;";
my $Version = "V.8.8";
my $Update = "2006-9-9 10:58";
my $modify = "genewise result only for one strand, not both.";
my $Version = "V.9.0";
my $Update = "2006-11-9 18:16";
my $modify = "debug rows with no indels, and with split codon.";
my $Version = "V.10.0";
my $Update = "2006-12-12 17:19";
my $modify = "debug entries with intron like indels, add int.";
my $Version = "V.10.2";
my $update = "2007-1-8 01:51";
my $modify = "debug two split codon in one line, or with small exons.";
#-------------------------------------------------------------------
#-------------------------------------------------------------------
use strict;
use Getopt::Long;
use Data::Dumper;
my %opts;
GetOptions(\%opts,"i:s","q:s","m:s","ot:s","os:s","ob:s","s:s","only","help");
if((!defined($opts{i}) || !defined($opts{q})) || defined($opts{help}) ){
Usage();
}
my $input = defined $opts{i} ? $opts{i} : "";
my $query_file = defined $opts{q} ? $opts{q} : "";
my $step = defined $opts{s} ? $opts{s} : "1";
my $middle_file = defined $opts{m} ? $opts{m} : "middle.out";
my $blat_format = defined $opts{ob} ? $opts{ob} : "genewise2blat.psl";
my $output_seq = defined $opts{os} ? $opts{os} : "multiple_sequence.out";
my $output_table = defined $opts{ot} ? $opts{ot} : "$middle_file.tab";
###############################
#
my $score_cutoff = 35;
#
###############################
if (($step != 0) && ($step != 1)) {
print "ERROR:\n-s only can be 0 or 1\n\n";
Usage();
}
Head();
my %query_len;
my $protein_name = '';
my $dna_name = '';
my $input_filename = (split(/\//,$input))[-1]; #added 2006-02-14 zhenghk
my $input_sort = "sort_$input_filename"; #modified 2006-02-14 zhenghk
if ($step == 1){
print "Step 1: Process for output_table and output_blat_format...\n";
LoadQueryLen($query_file,\%query_len);
SortGeneWise($input,$input_sort);
$/="genewise \$Name: ";
open(I,$input_sort)||die"open genewise output error [$input]!\n";
open(O,">$output_table")||die"output error [$output_table]\n";
open(M,">$middle_file")||die"output error [$middle_file]\n";
open(BLAT,">$blat_format") || die "output blat format error [$blat_format]\n";
while(<I>){
if ($_ eq 'genewise $Name: '){
next;
}
#print $_,"\n";
my $i=0;
my @temp = split(/genewise output\n/);
#print scalar @temp,"\n";
my @data;
my $output_tag = 0;
my $global_strand;
for(my $block_count=0;$block_count<@temp;$block_count++){
$output_tag = 0;
if($block_count == 0){
my @block = split(/\n/,$temp[$block_count]);
($protein_name) = $block[4]=~/Query protein\:\s+(\S+)/;
($dna_name) = $block[9]=~/Target Sequence\s+(\S+)/;
my ($temp_strand) = $block[10]=~/Strand\:\s+(\S+)/;
if ($temp_strand eq 'reverse'){
$global_strand = '-';
}
else {
$global_strand = '+';
}
#print $protein_name,"\t",$dna_name,"\n";
}
else {
analysis_block(\@temp,$block_count,\@{$data[$block_count]});
print M Dumper @{$data[1]};
if ($data[1]->[0] ne '') {
$output_tag = 1;
}
#print Dumper @{$data[1]};
if($data[1][0] ne ''){
print O "$data[1][0]\t$data[1][1]\t$data[1][9]\t$data[1][10]\t$data[1][5]\t$data[1][16]\t$data[1][11]\t$data[1][3]\t$data[1][4]\t$data[1][12]\t$data[1][13]\n";
print BLAT "$query_len{$data[1][0]}\t0\t0\t0\t0\t0\t0\t0\t$global_strand\t$data[1][0]\t$query_len{$data[1][0]}\t$data[1][9]\t$data[1][10]\t$data[1][1]\t10000000\t$data[1][12]\t$data[1][13]\t$data[1][11]\t",join("\t",@{$data[1][17]}),"\n";
}
if ($block_count == 2){
warn "genewise format error\n";
exit;
}
}
}
if ($output_tag == 1) {
print M "//\n";
}
else {
warn "Warnning: GeneWise Score between $protein_name and $dna_name is lower than $score_cutoff!\n";
}
}
close M;
close O;
close BLAT;
if (!defined $opts{only}){
$step++;
}
}
if ($step == 2) {
print "\nStep 2: Process for output of multiple sequence alignment format...\n\n";
MultipleSeq($middle_file,$output_seq);
}
##### sub functions:
sub SortGeneWise {
my ($input,$output) = @_;
my %out;
my %relation;
$/="genewise \$Name:";
open(I,$input)||die "Can't open genewise input file[$input]!\n";
open(O,">$output")||die "Can't output sort-genewise file[$output]!\n";
while(<I>){
if ($_ eq 'genewise $Name:'){
next;
}
my ($name) = $_=~/Target Sequence\s+(\S+)/; #modify 2006-02-14
my ($pro_name) = $_=~/Query protein\:\s+(\S+)/; #added 2006-02-14
$relation{$name} = $pro_name;
#print $name,"\n";
$_ =~s/genewise \$Name:$//;
$_= "genewise \$Name:".$_;
if (exists $out{$name}){
print $name,"\n";
print $out{$name};
print $_,"\n";
$out{$name} = $_;
}
else {
$out{$name} = $_;
}
}
#print Dumper %relation;
foreach (sort {$relation{$a} cmp $relation{$b}} keys %relation){
#print $_,"\n";
print O $out{$_};
}
close I;
close O;
}
sub analysis_block {
my ($r_temp,$block_count,$r_return) = @_;
my $i = 0;
my @block = split(/\n/,$$r_temp[$block_count]);
my ($score) = $block[0]=~/Score (\S+) bits over entire alignment/;
my %space;
my @lost_codon_info;
my $protein_seq = LoadProSeq(\@block,\%space);
#print Dumper %space;
my $exact_match_seq = LoadMatchSeq(\@block);
my $aligned_dna_seq = LoadDNAnuclicSeq(\@block,\%space);
my $dna_translate_seq = LoadDNAtranslateSeq(\@block,\$i,\%space,\@lost_codon_info); # 2004-11-17 11:46 add an array @lost_codon_info;
#print Dumper @lost_codon_info;
##### Judge stop codon and frame shift
my $stop_codon = 0;
my $frame_shift = 0;
my $shift_join = '';
my $stop_join = '';
if ($dna_translate_seq=~/X/){
my $tmp_dna = $dna_translate_seq;
my @stop_position;
subseq_positions($dna_translate_seq,"X",\@stop_position);
$stop_join = join("\:",@stop_position);
$stop_codon=1;
}
if ($dna_translate_seq=~/\!/){
my $tmp_dna = $dna_translate_seq;
my @shift_position;
subseq_positions($dna_translate_seq,"!",\@shift_position);
$shift_join = join("\:",@shift_position);
$frame_shift=1;
}
#print $dna_translate_seq,"\n";
###### identity calculation
if ((length $protein_seq) == 0){
print "Something Error:",$protein_name,"\t",$dna_name,"!!!\n";
exit;
}
my $no_gap_protein_seq = $protein_seq;
$no_gap_protein_seq =~s/-//g;
#my $identity = int (length($exact_match_seq)/length($protein_seq) * 10000 + 0.5) / 100;
my $identity = int (length($exact_match_seq)/length($no_gap_protein_seq) * 10000 + 0.5) / 100;
##### output
if($score > $score_cutoff){
#print Dumper %space;
#print "$protein_name\t$dna_name\t$score\t$frame_shift\t$stop_codon\t$identity\n";
#print $protein_seq,"\n";
#print $dna_translate_seq,"\n";
#my %FrameShiftInfo;
#GetFrameShiftInfo(\$aligned_dna_seq,\%FrameShiftInfo);
#print Dumper %FrameShiftInfo;
my @position;
my @dna_posi;
my @exon_len;
my %phase_exon;
my @blat_data;
my $exon_num = CountExon(\@block,$i,$block_count,\@position,\@dna_posi,\@exon_len,\%phase_exon,\@blat_data);
#print Dumper @blat_data;
#print Dumper @position;
#print Dumper @dna_posi;
#print Dumper @exon_len;
#RemoveFrameShiftLen(\%FrameShiftInfo,\@exon_len);
#print Dumper @exon_len;
#print Dumper @lost_codon_info;
#print $protein_seq,"\n";
#print $dna_translate_seq,"\n";
#print $aligned_dna_seq,"\n";
#print "=============\n";
DealSplitCodon(\$protein_seq,\$dna_translate_seq,\$aligned_dna_seq,\@exon_len,\%phase_exon,\@lost_codon_info);
#print $protein_seq,"\n";
#print $dna_translate_seq,"\n";
#print $aligned_dna_seq,"\n";
#print "=============\n";
# modify zhenghk 2004-7-2 13:45
# modify zhenghk 2004-10-26 14:47 modify "!" deletion bug!
# modify zhenghk 2005-3-17 10:45, deal with the frameshift in the sub function CountExon();
#my $copy_dna_translate_seq = $dna_translate_seq;
#my ($disruption_frame) = $copy_dna_translate_seq =~s/\!//g;
#$exon_num -= $disruption_frame;
$$r_return[0]=$protein_name;
$$r_return[1]=$dna_name;
$$r_return[2]=$score;
$$r_return[3]=$frame_shift;
$$r_return[4]=$stop_codon;
$$r_return[5]=$identity;
$$r_return[6]=$protein_seq;
$$r_return[7]=$dna_translate_seq;
$$r_return[8]=$aligned_dna_seq;
$$r_return[9]=$position[0];
$$r_return[10]=$position[-1];
$$r_return[11]=$exon_num;
$$r_return[12]=$dna_posi[0];
$$r_return[13]=$dna_posi[-1];
$$r_return[14]=$stop_join;
$$r_return[15]=$shift_join;
$$r_return[16]=int(($position[-1]-$position[0])/$query_len{$protein_name}*10000+0.5)/100;
$$r_return[17][0]=$blat_data[0];
$$r_return[17][1]=$blat_data[1];
$$r_return[17][2]=$blat_data[2];
$$r_return[17][3]=$blat_data[3];
}
}
sub GetFrameShiftInfo {
my ($r_seq,$r_info) = @_;
my $seq_copy = $$r_seq;
my (@frame_len) = $seq_copy =~/(\d+)/g;
my @sub_seq = split(/\d+/,$$r_seq);
my $position = '';
for(my $i=0;$i<@frame_len;$i++) {
if ($i>0){
$position += (length $sub_seq[$i]) + (length $frame_len[$i-1]);
}
else {
$position += (length $sub_seq[$i]);
}
$$r_info{$position} = $frame_len[$i];
}
}
sub RemoveFrameShiftLen {
my ($r_frame_info,$r_exon_len) = @_;
foreach my $position (keys %$r_frame_info) {
if ($$r_frame_info{$position} < 3){
next;
}
else {
my $exon_start = 1;
for(my $i=0;$i<@$r_exon_len;$i++){
if (($position/3) > $exon_start && ($position/3) < $$r_exon_len[$i]) {
$$r_exon_len[$i] -= int($$r_frame_info{$position}/3);
}
$exon_start = $$r_exon_len[$i] + 1;
}
}
}
}
sub subseq_positions {
my ($seq,$sub_seq,$r_posi) = @_;
if ($sub_seq eq '@'){
print "Sub seq can not be \@\n";
exit;
}
my (@space) = $seq=~/$sub_seq/g;
my $i = 0;
foreach (@space){
#print $_,"\n";
my $target = '@' x (length $_);
$$r_posi[$i++] = index($seq,$_);
$seq =~ s/$_/$target/;
#print $seq,"\n";
}
}
sub LoadProSeq {
my ($r_block,$r_space)=@_;
##### protein sequence
my $protein_seq = '';
for(my $i=6,my $j=0;$i<@$r_block;$i+=8,$j++){
if($$r_block[$i]=~/\/\//){
last;
}
my $sub_seq = substr($$r_block[$i],21,49);
#print $sub_seq,"<<<===\n";
my (@space) = $sub_seq=~/(\s+)/g;
foreach (@space){
my $target = 'B' x (length $_);
$$r_space{$j}->{index($sub_seq,$_)} = (length $_);
$sub_seq =~ s/$_/$target/;
}
$protein_seq .= $sub_seq;
}
$protein_seq =~s/B//g;
return $protein_seq;
}
sub LoadMatchSeq {
my ($r_block) = @_;
##### Match seqeunce
my $match_seq = '';
for(my $i=7;$i<@$r_block;$i+=8){
if($$r_block[$i]=~/^Gene/){
last;
}
$match_seq .= substr($$r_block[$i],21,49);
}
$match_seq =~s/\s//g;
my $exact_match_seq = $match_seq;
$exact_match_seq =~s/\+//g;
return $exact_match_seq;
}
sub LoadDNAtranslateSeq {
my ($r_block,$r_i,$r_space,$r_lost_codon) = @_;
##### DNA translate sequences
my $i = 0;
my $dna_translate_seq = '';
my $lost_count = 0;
my $save_last_lost_codon;
#print Dumper %$r_space;
for($i=8,my $j=0;$i<@$r_block;$i+=8,$j++){
if($$r_block[$i]=~/^Gene/){
last;
}
my $sub_seq = substr($$r_block[$i],21,49);
#print "1:[$sub_seq]\n";
#print "[$j]\n";
if(exists $$r_space{$j}){
#print "Line num: [$j]\n";
#print Dumper %{$$r_space{$j}};
foreach my $start (sort {$$r_space{$j}->{$b} <=> $$r_space{$j}->{$a}} keys %{$$r_space{$j}}){
my $space = substr($sub_seq,$start,$$r_space{$j}->{$start});
#print "[$space]\n";
my $target = 'B' x (length $space);
#print $target,"==>>>\n";
#print $sub_seq,"<<<\n";
$space = quotemeta($space);
$sub_seq=~tr/ /B/;
#print $sub_seq,">>>\n";
}
#print "2:[$sub_seq]\n";
foreach my $start (sort {$a <=> $b} keys %{$$r_space{$j}}){
my $space = substr($sub_seq,$start,$$r_space{$j}->{$start});
my @lost_codon_array;
my $lost_codon;
#print $space,"\n";
my $space_back = $space;
(@lost_codon_array) = $space_back =~/([^B]\:[^B]\[[^B]+\])/g;
if (@lost_codon_array > 1) { # added by zhenghk 2007-1-8 01:51; Version 10.2;
warn "\nWARNING!!! Small exon exists in the genewise alignment, please check it carefully!\n";
warn "$sub_seq\n";
}
$lost_codon = $lost_codon_array[0];
#print "Lost codon: [$lost_codon]\n";
#print "Exon num: [$lost_count]\n";
if ($$r_space{$j}->{$start} + $start == 49){ # modify skip end space, 2004-11-19 21:39;
############### added by zhenghk Version 10.2
if (@lost_codon_array > 1) {
$$r_lost_codon[$lost_count] = $lost_codon_array[0];
$lost_count++;
$$r_lost_codon[$lost_count] = $lost_codon_array[1];
}
else {
$$r_lost_codon[$lost_count] = $lost_codon;
}
my $next_gap_start;
if (exists $$r_space{$j+1}) {
$next_gap_start = (sort {$a <=> $b} keys %{$$r_space{$j+1}})[0];
}
#print "End is 49: next start is [$next_gap_start]\n";
if ($next_gap_start != 0){
$lost_count++;
}
}
elsif($start == 0) {
my $last_gap_start = (sort {$a <=> $b} keys %{$$r_space{$j-1}})[-1];
my $last_gap_end;
if (exists $$r_space{$j-1}) {
$last_gap_end = $last_gap_start + $$r_space{$j-1}->{$last_gap_start};
}
#print "Start is 0: last end is [$last_gap_end]\n";
if ($last_gap_end == 49){
if ($$r_lost_codon[$lost_count] eq '') {
#print "in\n";
#$$r_lost_codon[$lost_count] = $lost_codon;
############### added by zhenghk Version 10.2
if (@lost_codon_array > 1) {
$$r_lost_codon[$lost_count] = $lost_codon_array[0];
$lost_count++;
$$r_lost_codon[$lost_count] = $lost_codon_array[1];
}
else {
$$r_lost_codon[$lost_count] = $lost_codon;
}
}
}
else {
#$$r_lost_codon[$lost_count] = $lost_codon;
############### added by zhenghk Version 10.2
if (@lost_codon_array > 1) {
$$r_lost_codon[$lost_count] = $lost_codon_array[0];
$lost_count++;
$$r_lost_codon[$lost_count] = $lost_codon_array[1];
}
else {
$$r_lost_codon[$lost_count] = $lost_codon;
}
}
$lost_count++;
}
else {
#$$r_lost_codon[$lost_count] = $lost_codon;
############### added by zhenghk Version 10.2
if (@lost_codon_array > 1) {
$$r_lost_codon[$lost_count] = $lost_codon_array[0];
$lost_count++;
$$r_lost_codon[$lost_count] = $lost_codon_array[1];
}
else {
$$r_lost_codon[$lost_count] = $lost_codon;
}
$lost_count++;
}
$save_last_lost_codon=$lost_codon;
if ($lost_codon ne '') {
my $target = 'B' x 8;
#print "[$lost_codon] [$target]============================\n";
$lost_codon = quotemeta($lost_codon);
$sub_seq=~s/$lost_codon/$target/;
#print "[$sub_seq]\n";
if (@lost_codon_array > 1) {
$lost_codon_array[1] = quotemeta($lost_codon_array[1]);
$sub_seq=~s/$lost_codon_array[1]/$target/;
}
}
}
#print "3:[$sub_seq]\n";
}
else { #added zhenghk 2006-11-9 18:15; version 9.0; dealwith rows with no indels;
#print "$j&&&&&&&&&&&&&&&\n";
if (exists $$r_space{$j-1}) {
#print "###########################\n";
#print Dumper %{$$r_space{$j-1}};
my $last_gap_start = (sort {$a <=> $b} keys %{$$r_space{$j-1}})[-1];
#print $last_gap_start,"++++++++++++++++++++++++\n";
if ($$r_space{$j-1}->{$last_gap_start} + $last_gap_start == 49){
#print "$save_last_lost_codon,===============\n";
$$r_lost_codon[$lost_count] = $save_last_lost_codon;
$lost_count++;
}
}
}
#print "[==$lost_count==]\n";
#print "[==$lost_codon==]\n";
$dna_translate_seq .= $sub_seq;
}
$dna_translate_seq =~s/B//g;
#print "[$dna_translate_seq]\n";
$$r_i = $i;
return $dna_translate_seq;
}
sub LoadDNAnuclicSeq {
my ($r_block,$r_space) = @_;
##### DNA nuclic sequences
my $i = 0;
my $dna_na_seq = '';
#print Dumper %{$r_space};
for($i=9,my $j=0;$i<@$r_block;$i+=8,$j++){
my @phase;
if($$r_block[$i]=~/^\s+Exon/){
last;
}
for(my $k=$i;$k-$i<3;$k++){
my $sub_seq = substr($$r_block[$k],21,49);
#print $sub_seq,">>>>>>>>\n";
if(exists $$r_space{$j}){
foreach my $start (sort {$$r_space{$j}->{$b} <=> $$r_space{$j}->{$a}} keys %{$$r_space{$j}}){
my $space = substr($sub_seq,$start,$$r_space{$j}->{$start});
#print $space,"<<<==\n";
my $target = 'B' x (length $space);
#print $target,"==>>>\n";
#print $sub_seq,"<<<\n";
# modify 2006-05-18 zhenghk, if the space is at the end of the sequences, reverse the subseq then substitute it;
if ($start + $$r_space{$j}->{$start} == 49) {
$sub_seq = reverse($sub_seq);
#print $sub_seq,"########reverse seq\n";
$space = reverse($space); #modify 2005-05-22 zhenghk;
$space = quotemeta($space);
$sub_seq=~s/$space/$target/;
$sub_seq = reverse($sub_seq);
}
else {
$space = quotemeta($space);
$sub_seq=~s/$space/$target/;
}
#print $sub_seq,">>>\n";
}
}
$sub_seq =~ s/B//g;
$sub_seq =~ s/ /-/g;
#print $sub_seq,"<<<===\n";
@{$phase[$k-$i]}=split(//,$sub_seq);
}
my $sub_dna_na_seq = '';
for(my $n=0;$n<@{$phase[0]};$n++){
for(my $k=0;$k<3;$k++){
$sub_dna_na_seq .= $phase[$k]->[$n];
}
}
#print $sub_dna_na_seq,"\n";
$dna_na_seq .= $sub_dna_na_seq;
}
$dna_na_seq =~s/B//g;
return $dna_na_seq;
}
sub CountExon {
#my ($r_block,$i,$block_count,$r_posi,$r_dna,$r_exon_len,$r_phase_exon,$r_QS,$r_QL,$r_SStart,$r_SStop) = @_;
my ($r_block,$i,$block_count,$r_posi,$r_dna,$r_exon_len,$r_phase_exon,$r_blat) = @_;
my $strand = '';
my $exon_num = 0;
my $start;
my $stop;
my $phase;
my @posi;
my %support_pro;
my %support_dna;
my %intron_like_insert;
my $exon_support_end = 0; # added 2005-3-16 15:06
my %unsupport_pro; # added 2005-3-16 15:06
my $gene_count = 0; # added 2005-3-17 10:19
my @pro_array; # added 2005-3-21 16:36 to deal with frameshift problem
my @dna_array; # added 2005-3-21 16:36 to deal with frameshift problem
##### count exon number
for($i-=1;$i<@$r_block;$i++){
if($$r_block[$i]=~/\/\//){
if (@pro_array > 0){
#print Dumper @pro_array;
#print Dumper @dna_array;
# added 2005-3-21 16:33 deal with frameshift problems
for(my $k=0;$k<@pro_array - 1;$k+=2){
$support_pro{$pro_array[$k]} = $pro_array[$k+1];
if ($dna_array[0] < $dna_array[-1]){
$support_dna{$dna_array[$k]} = $dna_array[$k+1];
}
else {
$support_dna{$dna_array[$k+1]} = $dna_array[$k];
}
}
#print $start,"\t",$stop,"\n";
#print Dumper %support_pro;
#print Dumper %support_dna;
my @sort_pro_start = sort {$a<=>$b} keys %support_pro;
my $blat_query_start = $sort_pro_start[0];
my $blat_query_len = $support_pro{$sort_pro_start[-1]} - $blat_query_start + 1;
if ($$r_blat[0] eq '') {
$$r_blat[0] = $blat_query_len.",";
$$r_blat[1] = $blat_query_start.",";
$$r_blat[2] = $start.",";
$$r_blat[3] = $stop.",";
}
else {
$$r_blat[0] .= $blat_query_len.",";
$$r_blat[1] .= $blat_query_start.",";
$$r_blat[2] .= $start.",";
$$r_blat[3] .= $stop.",";
}
#push(@$r_QS,$blat_query_start);
#push(@$r_QL,$blat_query_len);
#push(@$r_SStart,$start);
#push(@$r_SStop,$stop);
#print Dumper @$r_SStart;
GetIntronLikeGap(\%support_dna,$start,$stop,$phase,\%intron_like_insert);
#print Dumper %intron_like_insert;
print Dumper %unsupport_pro;
$$r_exon_len[$exon_num-1] = CountExonLen(\%support_pro,\%support_dna,\%intron_like_insert,\%unsupport_pro);
@pro_array = ();
@dna_array = ();
%support_pro = ();
%support_dna = ();
%intron_like_insert = ();
}
last;
}
if($$r_block[$i]=~/^\s+Exon/){
if ($gene_count > 1){
($stop) = $$r_block[$i]=~/\s+Exon\s+\d+\s+(\d+)\s+phase\s+\d+/;
#$gene_count = 1;
}
else {
if (@pro_array > 0){
#print "in================\n";
#print Dumper @pro_array;
#print Dumper @dna_array;
for(my $k=0;$k<@pro_array - 1;$k+=2){
$support_pro{$pro_array[$k]} = $pro_array[$k+1];
if ($dna_array[0] < $dna_array[-1]){
$support_dna{$dna_array[$k]} = $dna_array[$k+1];
}
else {
$support_dna{$dna_array[$k+1]} = $dna_array[$k];
}
}
#print "$$r_block[$i]\n";
#print $start,"\t",$stop,"\n";
#print Dumper %support_pro;
#print Dumper %support_dna;
my @sort_pro_start = sort {$a<=>$b} keys %support_pro;
my $blat_query_start = $sort_pro_start[0];
my $blat_query_len = $support_pro{$sort_pro_start[-1]} - $blat_query_start + 1;
if ($$r_blat[0] eq '') {
$$r_blat[0] = $blat_query_len.",";
$$r_blat[1] = $blat_query_start.",";
$$r_blat[2] = $start.",";
$$r_blat[3] = $stop.",";
}
else {
$$r_blat[0] .= $blat_query_len.",";
$$r_blat[1] .= $blat_query_start.",";
$$r_blat[2] .= $start.",";
$$r_blat[3] .= $stop.",";
}
#push(@$r_QS,$blat_query_start);
#push(@$r_QL,$blat_query_len);
#push(@$r_SStart,$start);
#push(@$r_SStop,$stop);
GetIntronLikeGap(\%support_dna,$start,$stop,$phase,\%intron_like_insert);
#print Dumper %intron_like_insert;
print Dumper %unsupport_pro;
$$r_exon_len[$exon_num-1] = CountExonLen(\%support_pro,\%support_dna,\%intron_like_insert,\%unsupport_pro);
@pro_array = ();
@dna_array = ();
%support_pro = ();
%support_dna = ();
%intron_like_insert = ();
}
($start,$stop,$phase)=$$r_block[$i]=~/\s+Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/; #add $phase by zhenghk 2004-11-5 14:53
#print $start,"\t",$stop,"\t++",$phase,"===============\n";
### save lost split codon dna position, zhenghk 2004-11-5 15:03
if ($phase > 0){
$$r_phase_exon{$exon_num}=1;
#print "====================\n";
}