=head 
#Perl script. 
#Author: Kishor Dhaygude. 
#Please save this text file in .pl format before running this script.
#GenomeThreader Software used for obtaining cDNA/EST based spliced alignments with C. floridanus genome.

#A)	Alignment of transcripts (Evidence-TA) with C. floridanus genome

Command used: /Software/gth-1.5.2-Linux_x86_64-64bit/bin/gth -intermediate -xmlout -gzip -o cflo.inter.gz -genomic cflo_v3.3.fa -cdna TAContigs.fasta -v

Where,
cflo_v3.3.fa= genome of C. floridanus.
TAContigs.fasta: Evidence-TA from this project assembly.

B) 	Self Blast of TA contigs against themselves to generate matrix of alignment. This matrix will be used for isoform prediction.

#kmr25_comp62777_c0_seq1	2356	kmr29_comp88609_c0_seq3		2810	113	1.000	6.5162e-53	0.05	0.04
#kmr25_comp62777_c0_seq1	2356	kmr29_comp88609_c0_seq4		2771	113	1.000	6.5162e-53	0.05	0.04
#kmr25_comp62777_c0_seq1	2356	kmr29_comp88609_c0_seq1		2891	113	1.000	6.5162e-53	0.05	0.04

#Save this output as blast_matrix_Input.txt 
	
#run following script on linux/mac terminal using following command.
#perl Script.pl blast_matrix_Input.txt >result_output.txt

#similar to this script: awk '{if($1!=temp && flag==1){print gene"\t"count"\t"name;count=0;name="";}temp=$1;flag=1;gene=$1;count++;name=name$3",";}' Isoform_Parse_blast_aln100.txt >Isoform_count.txt

#script start from after “=cut” word. All above line belong to comments.
=cut


%hash=();
%hash2=();
%Hash2=();
%Hash3=();
%Hash1=();
%Hash4=();
%Hash5=();
%hash6=();
%out=();
%out1=();
open(F,$ARGV[0]);
foreach(<F>)
{
chomp;
@L=split("\t",$_);

next if(exists $HASH{$L[2]} && $HASH1{$L[0]});

$hash{$L[0]}{$L[2]}="NA";
$HASH{$L[0]}++;
$HASH1{$L[2]}++;
}

############################################


			foreach $A(sort(keys(%hash)))
			{       
                             foreach $B(sort(keys(%{$hash{$A}})))
			   {       
                             $Hash{$B}{$A}++;
                           }
			}

################################################
open (OUT,">Isoform_TA.txt");
foreach $A(sort(keys(%hash)))
{       
      
    $count=0;   
          $name=();
              foreach $BB(sort(keys(%{$hash{$A}})))
			   { 
							     if(exists $Hash{$BB})
							      {
							      foreach $CC(sort(keys(%{$Hash{$BB}})))
								{
                                                                         if(!exists $OUT{$CC})
                                                                            {
                                                                               #$name.=$CC.",";
                                                                                print OUT $A,"\t",$CC,"\n";
		                                                               #$count++;  
                                                                             # $LAST{$A}{$CC}++ ;
                                                                               $OUT{$CC}++;  
                                                                            }
								}
							      }
                                     if( !exists $OUT{$BB})
                                           {
                                             #$name.=$BB.",";
                                       # $LAST{$A}{$BB}++;
                                         print OUT $A,"\t",$BB,"\n";
		                             $count++;   
                                             $OUT{$BB}++;  
                                           }
                          }

#if($count==0 && $OUT{$CC}++ )
#print $A,"\t",$count,"\t",$name,"\n";
}
`sort -k2,2 -k1,1 Isoform_TA.txt >Isoform_TA_sorted.txt`;
open(IN, "Isoform_TA_sorted.txt");
%Hash=();
foreach(<IN>)
{
chomp;

@Line=split("\t",$_);


if(exists $Hash{$Line[1]})
{
#print $Hash{$Line[1]},"\t",$Line[0],"\n";
push(@All,$Hash{$Line[1]});
push(@All2,$Line[0]);
$Hash{$Line[0]}=$Hash{$Line[1]};
}
else
{
#print $Line[0],"\t",$Line[1],"\n";
push(@All,$Line[0]);
push(@All2,$Line[1]);
$Hash{$Line[1]}=$Line[0];
}
			
}

######################################
for($k=0;$k<=$#All;$k++)
{
if(exists $Hash{$All[$k]})
{
$All[$k]=$Hash{$All[$k]};
$Hash{$All2[$k]}=$Hash{$All[$k]};
}
#print $All[$k],"\t",$All2[$k],"\n";

$gene{$All[$k]}.=$All2[$k].",";
$count{$All[$k]}++;
}



############################################

foreach $X(sort(keys(%gene)))
{
print $X,"\t",$count{$X},"\t",$gene{$X},"\n";
}
exit(0);

######################################################