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190bisbis #203

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merged 3 commits into from Nov 29, 2021
Merged

190bisbis #203

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51c48c3
fix #190 - error in handling location B after location A
Juke34 Nov 22, 2021
f78a82f
fix #190. The script was still bugged. Now it sounds fine
Juke34 Nov 29, 2021
1c6ca9b
Merge branch 'master' into 190bisbis
Juke34 Nov 29, 2021
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143 changes: 65 additions & 78 deletions bin/agat_sp_sensitivity_specificity.pl
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Expand Up @@ -248,15 +248,14 @@
# keep track last locationA
my $last_locationA = undef;
$last_locationA = 1 if (scalar @{$flattened_locations1->{$locusID}{$chimere_type}{$level}{$type}} == 0);
print "Last LocationA !!\n" if ( $last_locationA and $verbose);
print "Lets go for last LocationA !!\n" if ( $last_locationA and $verbose);

if ( exists_keys ($flattened_locations2, ($locusID,$chimere_type,$level,$type) ) and
scalar @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}} != 0 ){ # and

my $previous_overlap = 0;
while ( scalar @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}} != 0 ){
if ($verbose) { print " list of location2 $level $type: "; foreach my $array ( @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}}){print "@{$array} - "; } print "\n";}
my $shift_it = 1;

my $location2 = $flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}->[0];
print " location2 investigated: @$location2\n" if ($verbose);
print " Original TP: ".$all{$chimere_type}{$level}{$type}{'TP'}."\n" if $verbose;
Expand All @@ -266,110 +265,117 @@
# keep track last locationA
my $last_locationB = undef;
$last_locationB = 1 if (scalar @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}} == 1);
print " Last LocationB !!\n" if ($last_locationB and $verbose);
print " Lets go for last LocationB !!\n" if ($last_locationB and $verbose);

# ===================== CASE 1 =====================
# location A ----------------
# location B ---------------
if ($location2->[1] < $location1->[0]){
print " shift location2 because before location A!\n" if ($verbose);
my $FP = $location2->[1] - $location2->[0] + 1; #size
$all{$chimere_type}{$level}{$type}{'FP'} += $FP;
print " +FP => $FP\n" if ($verbose);
$previous_overlap = 0;
$all{$chimere_type}{$level}{$type}{'FP'} += $FP;

print "End1 TP: ".$all{$chimere_type}{$level}{$type}{'TP'}."\n" if $verbose;
print "End1 FN: ".$all{$chimere_type}{$level}{$type}{'FN'}."\n" if $verbose;
print "End1 FP: ".$all{$chimere_type}{$level}{$type}{'FP'}."\n" if $verbose;
print " Case1 - Next location2!\n\n" if ($verbose);
my $tothrow = shift @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}};# Throw location B
}


# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# ------------ OVERLAP -----------
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
elsif( ($location1->[0] <= $location2->[1]) and ($location1->[1] >= $location2->[0])){
$previous_overlap = 1;
print " location @$location1 and @$location2 overlap !!!!\n" if $verbose;
my ($FN, $FP, $TP) = get_snsp_for_overlaps ($location1, $location2);
print " FN=$FN, FP=$FP, TP=$TP\n" if $verbose;


my $locationB_remain = 0 ;
my $locationA_remain = 0 ;
# check vvvv
# location A -------
# location B --------------
# but only if not the last location
my $locationB_remain = 0 ;
my $locationA_remain = 0 ;
my $clean_cut = 0 ;
if( $location2->[1] > $location1->[1] ){
$locationB_remain = $location2->[1] - $location1->[1] + 1;
$shift_it = undef;
}
# check vvvv
# location A -----------
# location B --------------
elsif( $location1->[1] > $location2->[1] ){
$locationA_remain = 1;
}
# v
# location A -------- <
# location B -------------- <
else{
$clean_cut = 1;
}

# location A -------------
# location B ----------- -- ------------

print "locationA_remain $locationA_remain \n" if $verbose;
print "locationB_remain $locationB_remain \n" if $verbose;
print "clean_cut $clean_cut \n" if $verbose;
if ($locationA_remain and !$last_locationA){

if ($locationA_remain and !$last_locationA and !$last_locationB){
# TP must always be added
$all{$chimere_type}{$level}{$type}{'TP'} += $TP;
$all{$chimere_type}{$level}{$type}{'FN'} -= $TP;
$all{$chimere_type}{$level}{$type}{'FP'} += $FP;
print " TP: ADDING ".$TP."\n" if $verbose;
print " FN: removing ".$TP."\n" if $verbose;
print " FP: ADDING ".$FP."\n" if $verbose;
print " TP: ADDING ".$TP."\n" if $verbose;
print " Case2 A - Next location B \n" if $verbose;
my $tothrow = shift @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}};# Throw location B
}
elsif ($locationB_remain and !$last_locationB){

elsif ($locationB_remain and !$last_locationA and !$last_locationB){
# TP must always be added
$all{$chimere_type}{$level}{$type}{'TP'} += $TP;
$all{$chimere_type}{$level}{$type}{'FN'} += $FN;
$all{$chimere_type}{$level}{$type}{'FP'} -= $TP;

print " TP: ADDING ".$TP."\n" if $verbose;
print " FN: ADDING ".$FN."\n" if $verbose;
print " FP: removing ".$TP."\n" if $verbose;
print " TP: ADDING ".$TP."\n" if $verbose;
print " Case2 B - Next location A\n" if $verbose;
last;
}
else{

else{ #clean cut or end of one type of location (1 or 2)
$all{$chimere_type}{$level}{$type}{'FN'} += $FN;
$all{$chimere_type}{$level}{$type}{'FP'} += $FP;
$all{$chimere_type}{$level}{$type}{'TP'} += $TP;
print " TP: ADDING ".$TP."\n" if $verbose;
print " FN: ADDING ".$FN."\n" if $verbose;
print " FP: ADDING ".$FP."\n" if $verbose;
print " TP: ADDING ".$TP."\n" if $verbose;
}

# From previous locationA analysis
if($locationB_remain){
# No more locationA
if( $last_locationA ){
print " No more location A 1\n" if $verbose;
# No more locationB
if( $last_locationB ){
print " No more location B\n" if $verbose;
print " Case2 C ------\n" if $verbose;
print " End TP: ".$all{$chimere_type}{$level}{$type}{'TP'}."\n" if $verbose;
print " End FN: ".$all{$chimere_type}{$level}{$type}{'FN'}."\n" if $verbose;
print " End FP: ".$all{$chimere_type}{$level}{$type}{'FP'}."\n\n" if $verbose;

if( $last_locationB and !$last_locationA){
print " Case2 C2 - Remove last location B\n" if ($verbose);
my $tothrow = shift @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}};# Throw location B
}
elsif ($last_locationA and !$last_locationB){
print " Case2 C3 - No more location A - LAST\n" if $verbose;
last;
}
elsif ($last_locationA and $last_locationB){
print " Case2 C4 - No more locationA neither locationB. Removing locationB and LAST.\n" if ($verbose);
my $tothrow = shift @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}};# Throw location B
last;
}
# clean cut v
# location A -------- <
# location B -------------- <
# No more locationA
elsif(!$locationA_remain and !$locationB_remain){
print " Clean cut !!! Removing LocationB and next Location A\n" if $verbose;
my $tothrow = shift @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}};# Throw location B
last; # next locationA
}
print " Next location B\n" if $verbose;
$shift_it = 1;
}
else{
print " Next location A\n" if $verbose;
last; # next locationA
}
}
elsif( $clean_cut ){
print " Clean cut !!! Removing LocationB and next Location A\n" if $verbose;
my $tothrow = shift @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}};# Throw location B
print " End3 TP: ".$all{$chimere_type}{$level}{$type}{'TP'}."\n" if $verbose;
print " End3 FN: ".$all{$chimere_type}{$level}{$type}{'FN'}."\n" if $verbose;
print " End3 FP: ".$all{$chimere_type}{$level}{$type}{'FP'}."\n\n" if $verbose;
last; # next locationA
}
}

# ===================== CASE 3 =====================
# location A -------------------------
# location B -------------------------
else{
Expand All @@ -378,43 +384,23 @@
my $FN = $location1->[1] - $location1->[0] + 1; #size
$all{$chimere_type}{$level}{$type}{'FN'} += $FN;
print " Take into account the current locationA! +FN: $FN;\n" if ($verbose);
$shift_it = undef;

print "End2 TP: ".$all{$chimere_type}{$level}{$type}{'TP'}."\n" if $verbose;
print "End2 FN: ".$all{$chimere_type}{$level}{$type}{'FN'}."\n" if $verbose;
print "End2 FP: ".$all{$chimere_type}{$level}{$type}{'FP'}."\n\n" if $verbose;


# no more location1
if(scalar @{$flattened_locations1->{$locusID}{$chimere_type}{$level}{$type}} == 0 ){
my $tothrow = shift @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}};# Throw location B
print "No more location A 2\n" if $verbose;
next;
}
else{
$previous_overlap = 0;
last; # next locationA
}
}

#
# - END -
#
if ($shift_it){
my $tothrow = shift @{$flattened_locations2->{$locusID}{$chimere_type}{$level}{$type}};# Throw location B
print " Removing location2: @$tothrow\n" if ($verbose);
print " End2 TP: ".$all{$chimere_type}{$level}{$type}{'TP'}."\n" if $verbose;
print " End2 FN: ".$all{$chimere_type}{$level}{$type}{'FN'}."\n" if $verbose;
print " End2 FP: ".$all{$chimere_type}{$level}{$type}{'FP'}."\n" if $verbose;
print " Case3 - Next location A \n\n" if $verbose;
last; # next locationA
}
print "End1 TP: ".$all{$chimere_type}{$level}{$type}{'TP'}."\n" if $verbose;
print "End1 FN: ".$all{$chimere_type}{$level}{$type}{'FN'}."\n" if $verbose;
print "End1 FP: ".$all{$chimere_type}{$level}{$type}{'FP'}."\n\n" if $verbose;
}# END WHILE until location B is after A
}

# ===================== CASE 4 =====================
# The list of locationB is empty now
else{
my $FN += $location1->[1] - $location1->[0] + 1; #size
print " LocationA only => +FN:$FN\n" if ($verbose);
$all{$chimere_type}{$level}{$type}{'FN'} += $FN;
print " Case4 - Next location A \n\n" if $verbose;
}
}
}
Expand All @@ -425,6 +411,7 @@
my $FN=0;
foreach my $location ( @{$flattened_locations1->{$locusID}{$chimere_type}{$level}{$type}} ){ # here the location are supposed to be sorted
$FN += $location->[1] - $location->[0] + 1; #size
print " Case5 - Next location A \n" if $verbose;
}
$all{$chimere_type}{$level}{$type}{'FN'} += $FN;
}
Expand Down
24 changes: 22 additions & 2 deletions t/scripts_output.t
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Expand Up @@ -4,7 +4,7 @@ use strict;
use warnings;
use File::Path;

use Test::More tests => 58;
use Test::More tests => 61;

=head1 DESCRIPTION

Expand Down Expand Up @@ -486,11 +486,31 @@ unlink $outtmp;

$script = $script_prefix."bin/agat_sp_sensitivity_specificity.pl";
$result = "$output_folder/agat_sp_sensitivity_specificity_2.txt";
system(" $script --gff1 $input_folder/agat_sp_sensitivity_specificity/1.gff --gff2 $input_folder/agat_sp_sensitivity_specificity/2.gff -o $outtmp 2>&1 1>/dev/null");
system(" $script --gff1 $input_folder/agat_sp_sensitivity_specificity/ref0.gff3 --gff2 $input_folder/agat_sp_sensitivity_specificity/query0.gff3 -o $outtmp 2>&1 1>/dev/null");
#run test
ok( system("diff $result $outtmp") == 0, "output $script");
unlink $outtmp;

$script = $script_prefix."bin/agat_sp_sensitivity_specificity.pl";
$result = "$output_folder/agat_sp_sensitivity_specificity_3.txt";
system(" $script --gff1 $input_folder/agat_sp_sensitivity_specificity/ref1.gff3 --gff2 $input_folder/agat_sp_sensitivity_specificity/query1.gff3 -o $outtmp 2>&1 1>/dev/null");
#run test
ok( system("diff $result $outtmp") == 0, "output $script");
unlink $outtmp;

$script = $script_prefix."bin/agat_sp_sensitivity_specificity.pl";
$result = "$output_folder/agat_sp_sensitivity_specificity_4.txt";
system(" $script --gff1 $input_folder/agat_sp_sensitivity_specificity/ref2.gff3 --gff2 $input_folder/agat_sp_sensitivity_specificity/query2.gff3 -o $outtmp 2>&1 1>/dev/null");
#run test
ok( system("diff $result $outtmp") == 0, "output $script");
unlink $outtmp;

$script = $script_prefix."bin/agat_sp_sensitivity_specificity.pl";
$result = "$output_folder/agat_sp_sensitivity_specificity_5.txt";
system(" $script --gff1 $input_folder/agat_sp_sensitivity_specificity/ref3.gff3 --gff2 $input_folder/agat_sp_sensitivity_specificity/query3.gff3 -o $outtmp 2>&1 1>/dev/null");
#run test
ok( system("diff $result $outtmp") == 0, "output $script");
unlink $outtmp;
# --------check agat_sp_split_by_level2_feature.pl-------------

$script = $script_prefix."bin/agat_sp_separate_by_record_type.pl";
Expand Down
0 ...put/agat_sp_sensitivity_specificity/2.gff → ...at_sp_sensitivity_specificity/query0.gff3
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File renamed without changes.