view call_consensus_from_sam_3.pl @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

#!/usr/bin/perl
# This calls a consensus based on the sam file and does not use qual scores etc it simply counts up each event and calls a simple most observations consensus
# the sam file must be sorted in order to cope with indels.
# usgae is ./call_consensus_from_sam_3.pl aligned.sam genome.fasta 10
# the number 10 is the minimum mapq you want to consider



open (INFILEFASTA, "$ARGV[1]"); # opens files

open (INFILESAM, "$ARGV[0]");
$full_len_cut = 1000;
$min_mapq = $ARGV[2];
$full_len_count = 0;
open (OUT, ">$ARGV[0].Observed_differences_list.txt");
open (OUTINDELS, ">$ARGV[0].Indels_applied_list.txt");
open (OUTMINOR, ">$ARGV[0].minor_variants.txt");
print OUTMINOR "Genome\tPosition\tA\tC\tG\tT\tDepth\n";
open (OUTMINORB, ">$ARGV[0].dominant_minor_variant.txt");
print OUTMINORB "Genome\tPosition\tA\tC\tG\tT\tDominat nucleotide\tFrequency\tTotal Depth\n";
print OUT "Genome\tPosition\tReference nucleotide\tGATC Depth count\tG count\tA count\tT count\tC count\tConsensus (. means no change from reference)\tDeletions\tTotal insertions recorded\tThis insertion most popular\tThis many recorded most popular insertions\n";
open (OUTNEWG, ">$ARGV[0].corrected_genome_snps_only.txt");
open (OUTNEWGINDEL, ">$ARGV[0].corrected_genome_snps_and_indels.txt");
open (OUTINDELKEY, ">$ARGV[0].key_indels.txt");
open (OUTINDELKEYSIG, ">$ARGV[0].Significant_key_indels.txt");
open (OUTFULLSAM, ">$ARGV[0].full_len_sam.sam");
$start_time = time;

%for_translation = (TTT=>"F", TTC=>"F", TCT=>"S", TCC=>"S", TAT=>"Y", TAC=>"Y", TGT=>"C", TGC=>"C", TTA=>"L", TCA=>"S", TAA=>"*", TGA=>"*", TTG=>"L", TCG=>"S", TAG=>"*", TGG=>"W", CTT=>"L", CTC=>"L", CCT=>"P", CCC=>"P", CAT=>"H", CAC=>"H", CGT=>"R", CGC=>"R", CTA=>"L", CTG=>"L", CCA=>"P", CCG=>"P", CAA=>"Q", CAG=>"Q", CGA=>"R", CGG=>"R", ATT=>"I", ATC=>"I", ACT=>"T", ACC=>"T", AAT=>"N", AAC=>"N", AGT=>"S", AGC=>"S", ATA=>"I", ACA=>"T", AAA=>"K", AGA=>"R", ATG=>"M", ACG=>"T", AAG=>"K", AGG=>"R", GTT=>"V", GTC=>"V", GCT=>"A", GCC=>"A", GAT=>"D", GAC=>"D", GGT=>"G", GGC=>"G", GTA=>"V", GTG=>"V", GCA=>"A", GCG=>"A", GAA=>"E", GAG=>"E", GGA=>"G", GGG=>"G");
%rev_translation = (GGC=>"A", ACT=>"S", TCA=>"*", ACA=>"C", TCG=>"R", GAT=>"I", GTT=>"N", GCT=>"S", GTA=>"Y", TGT=>"T", CGA=>"S", CGG=>"P", CAG=>"L", TGC=>"A", CAC=>"V", CTT=>"K", AAC=>"V", GTG=>"H", TCT=>"R", GGT=>"T", TGG=>"P", CCA=>"W", GAG=>"L", GCG=>"R", CAA=>"L", TTA=>"*", CTG=>"Q", CGT=>"T", CAT=>"M", TTT=>"K", TAC=>"V", CTA=>"*", AAG=>"L", TCC=>"G", GAC=>"V", GCA=>"C", TGA=>"S", AAT=>"I", ATA=>"Y", ATT=>"N", AGT=>"T", TTG=>"Q", GTC=>"D", ACC=>"G", GGA=>"S", AAA=>"F", CCT=>"R", ACG=>"R", CCG=>"R", ATG=>"H", TAT=>"I", GGG=>"P", CCC=>"G", TAA=>"L", CTC=>"E", TAG=>"L", ATC=>"D", AGA=>"S", GAA=>"F", CGC=>"A", GCC=>"G", AGC=>"A", TTC=>"E", AGG=>"P");
%base_pair = (G=>"A", A=>"T", T=>"A", C=>"G");

print OUTINDELS "Chromosome\tType\tLocation\tIndel_count\tIndel_size\tRead_depth\tIndel size\tIndel proportion\n";


%transcripts = ();
%orf_hash =();
%peptides_pep_score = ();
%unique_fastas = ();
%peptides_and_utn = ();
%utn_and_peptides = ();
%fasta_head_and_peptides = ();
%indel_tab = ();

$fasta_out ="";
$fasta_header = "Not_started_yet";
while ($fasta_line = <INFILEFASTA>)
{
    chomp $fasta_line;
    print "\n$fasta_line\n";
    if (substr($fasta_line,0,1) eq ">") {
        
        if ($fasta_header ne "Not_started_yet") {
            #print "\n\nFasta header $fasta_header\n\n";
            @temp = split (/\s+/, $fasta_header);
            $fasta_head_no_sp = $temp[0];
            #print "\n\nAfter split $fasta_head_no_sp\n\n";
            substr($fasta_head_no_sp,0,1) = "";
            $transcripts {$fasta_head_no_sp} = $fasta_out;
            
            #print "\n\n$fasta_head_no_sp\n\n";
        }
        
        
        $fasta_header = $fasta_line;
        
        
        $fasta_out ="";
    }
    if (substr($fasta_line,0,1) ne ">") {$fasta_out = $fasta_out.$fasta_line;}
}
($fasta_head_no_sp, $restofit) = split (/ /, $fasta_header);
substr($fasta_head_no_sp,0,1,"");
$transcripts {$fasta_head_no_sp} = $fasta_out;

#print "\n$fasta_header\n\n$fasta_head_no_sp\n";

$faster_header = "";
$chrom_proc = 0;
$chromosome = "notstartedyet";
$old_chromosome = "";
#exit;


$sam_count = 0;

$sam_header= "";
$transcript_count = 0;

open (INFILESAM, "$ARGV[0]");

while ($sam_line = <INFILESAM>)
{
    if (substr($sam_line,0,1) eq "@") {next;}
    #if (($sam_count % 10000) == 0) {print "$sam_count entries processed\n";}
    #print "$sam_count\n";
    $sam_count ++;
    chomp $sam_line;
    @sam_cells = split (/\t/, $sam_line);
    if ($sam_cells[2] eq "*") {next;}
    if (($sam_cells[2] ne $chromosome) and ($chromosome ne "notstartedyet")) {
        &process_data;
        $chromosome = $sam_cells[2];
        $genome = $transcripts{$chromosome};
        $len_gen = length $genome;
        delete $transcripts{$chromosome};
        $chrom_proc ++;
        print "hi $chromosome is being processed this is chromosome number $chrom_proc\n";
        %g = ();
        %a = ();
        %t = ();
        %c = ();
        %ins = ();
        %del = ();
        %depth = ();
        
    }
    # Data processed
    if ($chromosome eq "notstartedyet") {
        
        $chromosome = $sam_cells[2];
        $genome = $transcripts{$chromosome};
        $len_gen = length $genome;
        delete $transcripts{$chromosome};
        $chrom_proc ++;
        print "hi $chromosome is being processed this is chromosome number $chrom_proc\n";
        %g = ();
        %a = ();
        %t = ();
        %c = ();
        %ins = ();
        %del = ();
        %depth = ();

        
    }
    
    
    
    $utn = $sam_cells[0];
    $mapq = $sam_cells[4];
    $sequence = uc $sam_cells[9];
    $seq_len = length $sequence;
    $sequence =~ tr/Uu/TT/;
    #print "$sam_cells[5]\n";
    if ($min_mapq > $mapq) {next;}
    #print "OK";
    $flag = $sam_cells [1];
    $genome_position = $sam_cells[3] - 1;
    $fl_pos = $genome_position;
    if ($genome_position < $full_len_cut) {$full_len_flag = "S";
        #if (length $sequence > 28000) {print "possible full len\n";}
        
    } else {$full_len_flag = "I";}
    $sam_position  = 0;
    @cigar = split(/(M|I|D|N|S|H|P|X|=)/, $sam_cells[5]);
    $array_cigar = 1;
    $temp_len = 0;
    while (length($cigar[$array_cigar]) >=1){
        $cigar_value = $cigar[$array_cigar - 1];
        if (($cigar[$array_cigar] eq "M") or ($cigar[$array_cigar] eq "I") or ($cigar[$array_cigar] eq "S")){$temp_len = $temp_len + $cigar_value;}
        $array_cigar = $array_cigar + 2;
    }
    $tran_len = length $sequence;
    if ($tran_len ne $temp_len) {print "cigar fail\n";next;}
    $array_cigar = 1;
    while (length($cigar[$array_cigar]) >=1){
        #print "cigar entry is $cigar[$array_cigar]\n";
        $cigar_value = $cigar[$array_cigar - 1];
        if ($cigar[$array_cigar] =~ /[H]/){
            #nothing to do
        }
        if (($cigar[$array_cigar] =~ /[S]/) and (($array_cigar + 1) < scalar (@cigar)))
        {
            $soft_clip = $cigar_value;
            $sam_position = $sam_position + $cigar_value;
            $seq_len = $seq_len - $cigar_value;
        }
        
        
        if ($cigar[$array_cigar] =~ /[M]/){
            $temp_count = 1;
            #print "M";
            while ($temp_count <= $cigar_value)
            {
                $depth{$genome_position} ++;
                $alt = substr($sequence, $sam_position, 1);
                #print "alternative $alt\n";
                if ($alt eq "G") {$g{$genome_position} ++;}
                if ($alt eq "A") {$a{$genome_position} ++;}
                if ($alt eq "T") {$t{$genome_position} ++;}
                if ($alt eq "C") {$c{$genome_position} ++;}
                $temp_count ++;
                $genome_position ++;
                $sam_position ++;
                $fl_pos ++;
            }
        
        }

        #if (($cigar[$array_cigar] =~ /[D]/) and ($cigar_value >4)) {$cigar[$array_cigar] = "N";}
        
        if ($cigar[$array_cigar] =~ /[D]/){
            $temp_cv = $cigar_value - 1;
            $tmp_name = "$chromosome\tDeletion\t$genome_position\t$cigar_value\t ";
            if (exists $indel_tab{$tmp_name}){$indel_tab{$tmp_name} ++;} else {$indel_tab{$tmp_name} = 1;}
            while ($temp_cv >= 0){
            if (exists $del{$genome_position + $temp_cv}) {$del{$genome_position + $temp_cv} ++;} else {$del{$genome_position + $temp_cv} = 1;}
                $temp_cv --;
            }
            $genome_position = $genome_position + $cigar_value;
            $fl_pos = $fl_pos + $cigar_value;
        }
        
        if ($cigar[$array_cigar] =~ /[I]/){
            
            $insertion = substr ($sequence, $sam_position, $cigar_value);
            $tmp_name = "$chromosome\tInsertion\t$genome_position\t$cigar_value\t$insertion";
            if (exists $indel_tab{$tmp_name}){$indel_tab{$tmp_name} ++;} else {$indel_tab{$tmp_name} = 1;}
        if (exists $ins{$genome_position}) {$ins{$genome_position} = $ins{$genome_position}."\t$insertion";} else {$ins{$genome_position} = $insertion;}
        
            $sam_position = $sam_position + $cigar_value;
        
        }
        
        if ($cigar[$array_cigar] =~ /[N]/){
            
            $genome_position = $genome_position + $cigar_value;
            
        }
        $array_cigar = $array_cigar +2;
        
    }
    #if ($fl_pos > ($len_gen - 30)) {print "Stops\n";}
    #if (($fl_pos > ($len_gen - $full_len_cut)) and ($full_len_flag eq "S")) {print OUTFULLSAM "$sam_line\n"; print "Full length found\n"; $full_len_count ++;}
    if ($seq_len > ($len_gen - $full_len_cut)) {print OUTFULLSAM "$sam_line\n"; print "Full length found $seq_len X $len_gen\n"; $full_len_count ++;}
    
}




#all done just need to process the last chromosome...
&process_data;

foreach $keys (keys %transcripts){
    $genome = $transcripts{$keys};
    print OUTNEWGINDEL ">No_mapped_reads_to_".$keys."_genome_so_no_corrections\n$genome\n";
    print OUTNEWG ">No_mapped_reads_to_".$keys."_genome_so_no_corrections\n$genome\n";
}



$time_elapsed = time - $start_time;

print "Processed $sam_count entries for $chrom_proc chromosomes in $time_elapsed seconds\nFull length entries is $full_len_count\n";

exit;


sub process_data { #now to process all the data on this chromosome before moving on to the next one
    $genome_position = 0;
    $len_genome = length($genome);
    $old_genome = $genome;
    open (TEMP, ">temp.txt");
    
    
    while ($genome_position <= $len_genome){
        #print "at $genome_position\n";
        %ins_hash = ();
        %del_hash = ();
        $ref_nucleotide = substr ($genome, $genome_position, 1);
        $sam_con = $ref_nucleotide;
        $temp_pos = $genome_position + 1;
        
        if ($depth{$genome_position} > 0) {
        $A = $a{$genome_position}/$depth{$genome_position};
        $C = $c{$genome_position}/$depth{$genome_position};
        $G = $g{$genome_position}/$depth{$genome_position};
        $T = $t{$genome_position}/$depth{$genome_position};
        $test = -1;
        $consensus = "N";
        if ($A > $test){$test = $A; $consensus = "A";}
        if ($C > $test){$test = $C; $consensus = "C";}
        if ($G > $test){$test = $G; $consensus = "G";}
        if ($T > $test){$test = $T; $consensus = "T";}
        if ($consensus eq "A") {$A = $A * -1; $test = $A; print OUTMINOR "$chromosome\t$temp_pos\t$A\t$C\t$G\t$T\t$depth{$genome_position}\n";}
        if ($consensus eq "C") {$C = $C * -1; $test = $C; print OUTMINOR "$chromosome\t$temp_pos\t$A\t$C\t$G\t$T\t$depth{$genome_position}\n";}
        if ($consensus eq "G") {$G = $G * -1; $test = $G; print OUTMINOR "$chromosome\t$temp_pos\t$A\t$C\t$G\t$T\t$depth{$genome_position}\n";}
        if ($consensus eq "T") {$T = $T * -1; $test = $T; print OUTMINOR "$chromosome\t$temp_pos\t$A\t$C\t$G\t$T\t$depth{$genome_position}\n";}
        if ($consensus eq "N") {print OUTMINOR "$chromosome\t$temp_pos\t0\t0\t0\t0\n";}
            $major = $test * -1;
            if ($A > $test){$test = $A; $secconsensus = "A";}
            if ($C > $test){$test = $C; $secconsensus = "C";}
            if ($G > $test){$test = $G; $secconsensus = "G";}
            if ($T > $test){$test = $T; $secconsensus = "T";}
           
            if ($secconsensus eq "A") {print OUTMINORB "$chromosome\t$temp_pos\t$A\t0\t0\t0\t$consensus\t$major\t$depth{$genome_position}\n";}
            if ($secconsensus eq "C") {print OUTMINORB "$chromosome\t$temp_pos\t0\t$C\t0\t0\t$consensus\t$major\t$depth{$genome_position}\n";}
            if ($secconsensus eq "G") {print OUTMINORB "$chromosome\t$temp_pos\t0\t0\t$G\t0\t$consensus\t$major\t$depth{$genome_position}\n";}
            if ($secconsensus eq "T") {print OUTMINORB "$chromosome\t$temp_pos\t0\t0\t0\t$T\t$consensus\t$major\t$depth{$genome_position}\n";}
            if ($secconsensus eq "N") {print OUTMINORB "$chromosome\t$temp_pos\t0\t0\t0\t0\t$consensus\t$major\t$depth{$genome_position}\n";}
            
        } else {print OUTMINOR "$chromosome\t$temp_pos\t0\t0\t0\t0\n"; print OUTMINORB "$chromosome\t$temp_pos\t0\t0\t0\t0\n";}
        
        if ($depth{$genome_position} < 3) {
            if ($len_genome <100000){
                $sam_con = ".";
                print OUT "$chromosome\t$temp_pos\t$ref_nucleotide\t$depth{$genome_position}\t$g{$genome_position}\t$a{$genome_position} \t$t{$genome_position} \t$c{$genome_position}\t$sam_con\t$del{$genome_position}\t$ins_count\t$temp_most_ins\t$temp_most\n";
            }
            $genome_position ++;
            next;
        }
        
        $temp_most = 0;
        $temp_most_ins = "";
        $ins_count = 0;
        if (exists $ins{$genome_position}){
            $temp_ins = $ins{$genome_position};
            @insertions = split (/\t/, $temp_ins);
            $ins_count = scalar @insertions;
            foreach $key (@insertions)
            {
                $ins_hash{$key} ++;
                # print "found $key\n";
            }
            $temp_most = 0;
            $temp_most_ins = "";
            foreach $key (keys %ins_hash){
                # print "$key   $ins_hash{$key}\n";
                if ($ins_hash{$key} > $temp_most) {$temp_most = $ins_hash{$key}; $temp_most_ins = $key;}
            }
            
            
           
            #if ($ins_count > $depth{$genome_position}) {print OUT "POSSIBLE $ins_count INSERTION AT $genome_position\t $ins{$genome_position}\n";}
            if ($temp_most > ($depth{$genome_position}) ) {
                print OUT "Chromosome $chromosome TOTAL $ins_count INSERTION with $depth{$genome_position} no insertions AT $temp_pos most abundant is $temp_most_ins with $temp_most instertions\t $ins{$genome_position}\n";
                
                print TEMP "Chromosome $chromosome TOTAL $ins_count INSERTION with $depth{$genome_position} no insertions AT $temp_pos most abundant is $temp_most_ins with $temp_most instertions\t$temp_most_ins\t$genome_position\t$ins{$genome_position}\n";
            }
            if ($temp_most > (($depth{$genome_position})/10)) {
                $indel_proportion = $temp_most/$depth{$genome_position};
             #print OUTINDELS "Chromosome\tType\tLocation\tIndel_count\tIndel_size\tRead_depth\tIndel size\tIndel proportion\n";
            print OUTINDELS "$chromosome\tInsertion\t$genome_position\t$ins_count\t$temp_most_ins\t$depth{$genome_position}\t$temp_most_ins\t$indel_proportion\n";
            }
            
            
        }
        
        if (exists $del{$genome_position}){

            if ($del{$genome_position} > $depth{$genome_position}) {
                print OUT "Chromosome $chromosome POSSIBLE $del{$genome_position} deletion against $depth{$genome_position} no deletions found AT $temp_pos\n";
                #print OUTINDELS "Chromosome $chromosome POSSIBLE $del{$genome_position} deletion against $depth{$genome_position} no deletions found AT $temp_pos\n";
                print TEMP "Chromosome $chromosome POSSIBLE $del{$genome_position} deletion against $depth{$genome_position} no deletions found AT $temp_pos most frequent is $temp_most_dels deletion with $del{$genome_position}\t1\t$genome_position\t$del{$genome_position}\n";
            }
            #if ($del_count > 10) {print OUT "POSSIBLE $del_count deletion AT $genome_position\t $del{$genome_position}\n";}
            
            if ($del{$genome_position} > (($depth{$genome_position})/10)) {
                           $indel_proportion = $del{$genome_position}/$depth{$genome_position};
                        #print OUTINDELS "Chromosome\tType\tLocation\tIndel_count\tIndel_size\tRead_depth\tIndel size\tIndel proportion\n";
                       print OUTINDELS "$chromosome\tDeletion\t$genome_position\t$del{$genome_position}\t$temp_most_dels\t$depth{$genome_position}\t$temp_most_dels\t$indel_proportion\n";
                       }
            
            
        }
        
        
       
        
        
        
        $g_flag = 0;
        $a_flag = 0;
        $t_flag = 0;
        $c_flag = 0;
        $amb = "N";
        $top_nuc = 0;
        $top_nucleotide = "";
        $sec_nuc = 0;
        $second_nucleotide = "";
        $ref_nuc = 0;
        if ($ref_nucleotide eq "G") {$ref_nuc = $g{$genome_position};}
        if ($ref_nucleotide eq "A") {$ref_nuc = $a{$genome_position};}
        if ($ref_nucleotide eq "T") {$ref_nuc = $t{$genome_position};}
        if ($ref_nucleotide eq "C") {$ref_nuc = $c{$genome_position};}
        if ($g{$genome_position} >= $top_nuc){
            $sam_con = "G";
            #$g_flag = 1;
            $second_nucleotide = $top_nucleotide;
            $sec_nuc = $top_nuc;
            $top_nuc = $g{$genome_position};
            $top_nucleotide = "G";
            #if ($ref_nucleotide eq "G") {$amb ="G";}
        }
        if ($a{$genome_position} >= $top_nuc){
            $sam_con = "A";
            #$a_flag = 1;
            $second_nucleotide = $top_nucleotide;
            $sec_nuc = $top_nuc;
            $top_nuc = $a{$genome_position};
            $top_nucleotide = "A";
            #if ($ref_nucleotide eq "A") {$amb ="A";}
        }
        if ($t{$genome_position} >= $top_nuc){
                $sam_con = "T";
            #$t_flag = 1;
            $second_nucleotide = $top_nucleotide;
                $sec_nuc = $top_nuc;
                $top_nuc = $t{$genome_position};
            $top_nucleotide = "T";
            #    if ($ref_nucleotide eq "T") {$amb ="T";}
        }
        if ($c{$genome_position} >= $top_nuc){
                $sam_con = "C";
            #$c_flag = 1;
             $second_nucleotide = $top_nucleotide;
                $sec_nuc = $top_nuc;
                $top_nuc = $c{$genome_position};
             $top_nucleotide = "C";
            #    if ($ref_nucleotide eq "C") {$amb ="C";}
        }
        
        #print "This is G's recoded at this location $g{$genome_position}\n";
        if (($g{$genome_position} >= $a{$genome_position}) and ($g{$genome_position} >= $t{$genome_position}) and ($g{$genome_position} >= $c{$genome_position}) and ($g{$genome_position} >= 1)) {
            $sam_con = "G"; $g_flag = 1;
            if ($ref_nucleotide eq "G") {$amb ="G";}
        }
        if (($a{$genome_position} >= $g{$genome_position}) and ($a{$genome_position} >= $t{$genome_position}) and ($a{$genome_position} >= $c{$genome_position}) and ($a{$genome_position} >= 1)) {
            $sam_con = "A"; $a_flag = 1;
            if ($ref_nucleotide eq "A") {$amb ="A";}
        }
        if (($t{$genome_position} >= $g{$genome_position}) and ($t{$genome_position} >= $a{$genome_position}) and ($t{$genome_position} >= $c{$genome_position}) and ($t{$genome_position} >= 1)) {
            $sam_con = "T"; $t_flag = 1;
            if ($ref_nucleotide eq "T") {$amb ="T";}
        }
        if (($c{$genome_position} >= $g{$genome_position}) and ($c{$genome_position} >= $a{$genome_position}) and ($c{$genome_position} >= $t{$genome_position}) and ($c{$genome_position} >= 1)) {
            $sam_con = "C"; $c_flag = 1;
            if ($ref_nucleotide eq "C") {$amb ="C";}
        }
        
        if (($g_flag + $a_flag + $t_flag + $c_flag) > 1) {
            print OUT "ambiguity chromosome $chromosome at $temp_pos   $g_flag G $a_flag A $t_flag T $c_flag C counts are G $g{$genome_position} A $a{$genome_position} T $t{$genome_position} C $c{$genome_position} \n";
            if ($amb ne "N") {$sam_con = $amb;}
        }
        
        if ($sam_con ne $ref_nucleotide) {
            #print "change\n";
            print OUT "$chromosome\t$temp_pos\t$ref_nucleotide\t$depth{$genome_position}\t$g{$genome_position}\t$a{$genome_position} \t$t{$genome_position} \t$c{$genome_position}\t$sam_con\t$del{$genome_position}\t$ins_count\t$temp_most_ins\t$temp_most\n";
        } else {
            if (($len_genome <100000) or ($temp_most > $depth{$genome_position}) or ($del{$genome_position} > $depth{$genome_position})){
                print OUT "$chromosome\t$temp_pos\t$ref_nucleotide\t$depth{$genome_position}\t$g{$genome_position}\t$a{$genome_position} \t$t{$genome_position} \t$c{$genome_position}\t.\t$del{$genome_position}\t$ins_count\t$temp_most_ins\t$temp_most\n";
            }
        }
        
        
        substr ($genome, $genome_position, 1, $sam_con);
        
        $genome_position ++;
        #print "at second $genome_position\n";
        
    }
    
    
    close TEMP;
    $new_genome_w_indels = $genome;
    open (TEMP, "temp.txt");
    @indels = reverse<TEMP>;
    foreach $line (@indels)
    {
        chomp $line;
        @indels_cells = split(/\t/, $line);
        $change = $indels_cells[1];
        $type = $indels_cells[0];
        $genome_position = $indels_cells[2];
        if (index ($type, " INSERTION ") > 0) {
            substr ($new_genome_w_indels, $genome_position, 0, $change);
        }
        if (index ($type, " deletion ") > 0) {
            substr ($new_genome_w_indels, $genome_position, 1, "");
        }
        
    }
    
    
    
    print OUTNEWGINDEL ">New_".$chromosome."_genome_with_indels_is\n$new_genome_w_indels\n";
    print OUTNEWG ">New_".$chromosome."_genome_is\n$genome\n";
    open (CTSO, ">$ARGV[0].CTSO.txt");
    $warning = "";
    #open (OUTINDELKEYSIG, ">$ARGV[0].Significant_key_indels.txt");
    # open (OUTINDELKEY, ">$ARGV[0].key_indels.txt");
    # $tmp_name = "$chromosome\tDeletion\t$genome_position\t$temp_cv\t$insertion"; temp_cv is the size of the indel
    print OUTINDELKEY "Chromosome\tInsertion or deletion\tLocation\tIndel size\tInsertion seq\tObservation count\tDepth at this lcation\tProportion of observation vs depth\n";
    print OUTINDELKEYSIG "Chromosome\tInsertion or deletion\tLocation\tIndel size\tInsertion seq\tObservation count\tDepth at this lcation\tProportion of observation vs depth\n";
    foreach $key (keys %indel_tab){
        $value = $indel_tab{$key};
        @array = split(/\t/, $key);
        $genome_position = $array[2]; $indel_len = $array[3];
        if ($depth{$genome_position} > 0) {$a = ($value / $depth{$genome_position}); $tmp_proportion  = sprintf ("%.2f",$a);} else {$tmp_proportion = "zero depth here";}
 
           print OUTINDELKEY "$key\t$value\t$depth{$genome_position}\t$tmp_proportion\n";
           if ($tmp_proportion > 0.1) {
               
               if ($indel_len > 6) {print "\n\nCtSo\nInsertion or deletion\t$array[1]\nLocation\t$genome_position\nIndel size\t$indel_len\nObservation count\t$value\nDepth at this location\t$depth{$genome_position}\nProportion of observation vs depth\t$tmp_proportion\n\n";
                   print CTSO "\n\nCtSo\nInsertion or deletion\t$array[1]\nLocation\t$genome_position\nIndel size\t$indel_len\nObservation count\t$value\nDepth at this location\t$depth{$genome_position}\nProportion of observation vs depth\t$tmp_proportion\n\n";
                   print OUTINDELKEYSIG "$key\t$value\t$depth{$genome_position}\t$tmp_proportion\n";
                   if (($value > 9) or ($depth{$genome_position} > 9)) {$warning = $warning."$key\t$value\t$depth{$genome_position}\t$tmp_proportion\n";}
               }
               #print OUTINDELKEYSIG "$key\t$value\t$depth{$genome_position}\t$tmp_proportion\n";
           }
    
}
if ($warning ne "") {print OUTINDELKEYSIG "\n\nEspecially take a moment to look at these in the above list...CtSo!\n\n$warning\n";}
}