#!/usr/bin/env perl

use strict ;

use warnings ;

die "Usage: ./trust-barcoderep-to-10X.pl trust_barcode_report.tsv 10X_report_prefix\n" if (@ARGV == 0) ;

sub GetDetailChainType

{

    foreach my $g (@_)

    {

        if ( $g =~ /^IGH/ )

        {

            return 0 ;

        }

        elsif ( $g =~ /^IGK/ )

        {

            return 1 ;

        }

        elsif ( $g =~ /^IGL/ )

        {

            return 2 ;

        }

        elsif ( $g =~ /^TRA/ )

        {

            return 3 ;

        }

        elsif ( $g =~ /^TRB/ )

        {

            return 4 ;

        }

        elsif ( $g =~ /^TRG/ )

        {

            return 5 ;

        }

        elsif ( $g =~ /^TRD/ )

        {

            return 6 ;

        }

    }

    return 7 ;  

}

sub IsProductive

{

    my $aa = $_[0] ;

    return 0 if ($aa eq "partial" || $aa =~ /_/ || $aa =~ /\?/) ;

    return 1 ;

}

my @chainName = ("IGH", "IGK", "IGL", "TRA", "TRB", "TRG", "TRD", "None") ;

open FP, $ARGV[0] ;

my $prefix = $ARGV[1] ;

open FPoutT, ">".$prefix."_t.csv" ;

open FPoutB, ">".$prefix."_b.csv" ;

print FPoutT "barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id\n" ;

print FPoutB "barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id\n" ;

my $header = <FP> ;

while (<FP>)

{

    chomp ;

    my @cols = split ;

        #AACTCTTGTTATCCGA-1 abT *   TRAV6*01,*,TRAJ43*01,*,TGTGCTCTAGCCGGGGAGGGCATGCGCTTT,CALAGEGMRF,2.80,AACTCTTGTTATCCGA-1_26095,100.00   *   *

    for (my $i = 2 ; $i <= 3 ; ++$i)

    {

        next if ($cols[$i] eq "*") ;

        my @chainCols = split /,/, $cols[$i] ;

        #barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id

        #AAACCTGAGTCGATAA-1,True,AAACCTGAGTCGATAA-1_contig_1,True,551,IGK,IGKV1-5,None,IGKJ1,IGKC,True,True,CQQYNSYSRTF,TGCCAACAGTATAATAGTTATTCTCGAACGTTC,1197,22,clonotype77,clonotype77_consensus_2

        my @outputCols = ($cols[0], "True", "None", "True", "None", 

            $chainName[GetDetailChainType($chainCols[0], $chainCols[2],$chainCols[3])],

            $chainCols[0] eq "*" ? "None": $chainCols[0],

            $chainCols[1] eq "*" ? "None": $chainCols[1],

            $chainCols[2] eq "*" ? "None": $chainCols[2],

            $chainCols[3] eq "*" ? "None": $chainCols[3],

            "None", IsProductive($cols[5]) ? "True" : "False", 

            $chainCols[5], $chainCols[4], $chainCols[6], $chainCols[6], "None", "None"

            ) ;

        if (substr($cols[1], -1) eq "T")

        {

            print FPoutT join(",", @outputCols), "\n" ;

        }

        else

        {

            print FPoutB join(",", @outputCols), "\n" ;

        }

    }

}

close FPoutT ;

close FPoutB ;

close FP ;