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fix #435 - output list of IDs in files. Result is now a folder not an…
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…ymore a file
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@Juke34
Juke34 committed Mar 5, 2024
1 parent aa61c74 commit 8c67c49
Showing 1 changed file with 65 additions and 10 deletions.
75 changes: 65 additions & 10 deletions bin/agat_sp_compare_two_annotations.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -54,9 +54,22 @@
# --- Manage config ---
$config = get_agat_config({config_file_in => $config});

######################
# Manage output folder #

if (! $opt_output) {
print "Default output name: split_result\n";
$opt_output="comparison_result";
}

if (-d $opt_output){
print "The output directory choosen already exists. Please give me another Name.\n";exit();
}
mkdir $opt_output;

######################
# Manage output file #
my $report = prepare_fileout($opt_output);
my $report = prepare_fileout("$opt_output/report.txt");

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIN <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

Expand Down Expand Up @@ -323,7 +336,9 @@
my $flat_overlap_1 = $locations1;
my $flat_overlap_2 = $locations2;
my $overlap_A=1;
my @overlap_A_id=($locations1->[0][3]);
my $overlap_B=1;
my @overlap_B_id=($locations2->[0][3]);
my $loop="top";
my $flip=2;
my $current_locs;
Expand Down Expand Up @@ -372,9 +387,11 @@

if($loop eq "top"){
$overlap_A++;
push @overlap_A_id, $locations->[0][3];
}
elsif($loop eq "bot"){
$overlap_B++;
push @overlap_B_id, $locations->[0][3];
}
}
else{
Expand All @@ -398,14 +415,14 @@
}
}
}
$overlap_info{$locations1->[0][2]}{$overlap_A}{$overlap_B}++;
push @{$overlap_info{$locations1->[0][2]}{$overlap_A}{$overlap_B}}, [ [@overlap_A_id], [@overlap_B_id] ];
}
# ----------------------------------- CASE 1 -----------------------------------
# location A ----------------
# location B ---------------
elsif ($locations2->[scalar(@{$locations2})-1][1] < $locations1->[0][0] ){

$overlap_info{$locations1->[0][2]}{0}{1}++;
push @{$overlap_info{$locations1->[0][2]}{0}{1}}, [[undef], [$locations2->[0][3]]];
print "Case1 notoverlap !\n\n" if ($debug);
# throw loc2
remove_loc_by_id($flattened_locations2_clean_sorted, $locusID, $chimere_type, $locations2->[0][3]);
Expand All @@ -420,7 +437,7 @@
my $id1 = $locations1->[0][3];
print "Case2 notoverlap !\n" if ($debug);
if(! exists_keys(\%seen1, ( $id1 ) ) ){ # else it has been dealed by overlap case
$overlap_info{$locations1->[0][2]}{1}{0}++;
push @{$overlap_info{$locations1->[0][2]}{1}{0}}, [ [$locations1->[0][3]], [undef] ];
# throw loc1
remove_loc_by_id($flattened_locations1_clean_sorted, $locusID, $chimere_type, $id1);
$seen1{$id1}++;
Expand All @@ -442,7 +459,7 @@
foreach my $locusID ( keys %{$flattened_locations1_clean_sorted} ){
foreach my $chimere_type ( keys %{$flattened_locations1_clean_sorted->{$locusID}}){
foreach my $locations1 ( @{$flattened_locations1_clean_sorted->{$locusID}{$chimere_type}} ){
$overlap_info{$locations1->[0][2]}{1}{0}++;
push @{$overlap_info{$locations1->[0][2]}{1}{0}}, [ [$locations1->[0][3]], [undef]];
print " Case3 !\n" if ($debug);
}
}
Expand All @@ -454,7 +471,7 @@
foreach my $locusID ( keys %{$flattened_locations2_clean_sorted} ){
foreach my $chimere_type ( keys %{$flattened_locations2_clean_sorted->{$locusID}}){
foreach my $locations2 ( @{$flattened_locations2_clean_sorted->{$locusID}{$chimere_type}} ){
$overlap_info{$locations2->[0][2]}{0}{1}++;
push @{$overlap_info{$locations2->[0][2]}{0}{1}}, [ [undef], [$locations2->[0][3]] ];
print " Case4 !\n" if ($debug);
}
}
Expand Down Expand Up @@ -491,12 +508,50 @@
$total{$type_l1}{'B'}=0;
foreach my $value1 ( sort {$a <=> $b} keys %{$overlap_info{$type_l1}} ){
foreach my $value2 ( sort {$a <=> $b} keys %{$overlap_info{$type_l1}{$value1}} ){
$string_to_print .= "|".sizedPrint($value1,30)."|".sizedPrint($value2,30)."|".sizedPrint($overlap_info{$type_l1}{$value1}{$value2},30)."|\n";
if ($value1 != 0){
$total{$type_l1}{'A'} += $value1 * $overlap_info{$type_l1}{$value1}{$value2};
$string_to_print .= "|".sizedPrint($value1,30)."|".sizedPrint($value2,30)."|".sizedPrint(scalar(@{$overlap_info{$type_l1}{$value1}{$value2}}),30)."|\n";

# report ids
my $report_ids = prepare_fileout("$opt_output/$value1"."_".$value2."_id_list.txt");
# file1
foreach my $array ( @{$overlap_info{$type_l1}{$value1}{$value2}}) {
my $cpt=0;
my $last = scalar(@{$array->[0]});
foreach my $value ( @{$array->[0]} ) { # array0 is id overlarpA
$cpt++;
if(! $value){
print $report_ids "-";
} else {
if ($last == $cpt){
print $report_ids $value;
} else {
print $report_ids $value.", ";
}
}
}
print $report_ids " | ";
my $cpt2=0;
my $last2 = scalar(@{$array->[1]});
foreach my $value ( @{$array->[1]} ) { # array1 is id overlarpB
$cpt2++;
if(! $value){
print $report_ids "-\n";
} else {
if ($last2 == $cpt2){
print $report_ids "$value"
} else {
print $report_ids "$value, "
}
}
}
print $report_ids "\n";
}


if ($value1 != 0){
$total{$type_l1}{'A'} += $value1 * scalar(@{$overlap_info{$type_l1}{$value1}{$value2}});
}
if ($value2 != 0){
$total{$type_l1}{'B'} += $value2 * $overlap_info{$type_l1}{$value1}{$value2};
$total{$type_l1}{'B'} += $value2 * scalar(@{$overlap_info{$type_l1}{$value1}{$value2}});
}
}
}
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