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fix #471 + put features that cannot be checked because attribute is m…
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…issing in a separte file. The user can now decide to let these particular features aside or merge them back (manually) to one or the other output file
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@Juke34
Juke34 committed Jul 5, 2024
1 parent 9b9fa05 commit 92fee69
Showing 1 changed file with 93 additions and 55 deletions.
148 changes: 93 additions & 55 deletions bin/agat_sp_filter_feature_by_attribute_value.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@

###############
# Test options
if($opt_test ne "<" and $opt_test ne ">" and $opt_test ne "<=" and $opt_test ne ">=" and $opt_test ne "="){
if($opt_test ne "<" and $opt_test ne ">" and $opt_test ne "<=" and $opt_test ne ">=" and $opt_test ne "=" and $opt_test ne "!"){
print "The test to apply is Wrong: $opt_test.\nWe want something among this list: <,>,<=,>=,! or =.";exit;
}

Expand All @@ -70,19 +70,22 @@
my $gffout_ok_file ;
my $fhout_discarded_file ;
my $ostreamReport_file;
my $fhout_semidDiscarded_file;

if ($opt_output) {
my ($outfile,$path,$ext) = fileparse($opt_output,qr/\.[^.]*/);

# set file names
$gffout_ok_file = $path.$outfile.$ext;
$fhout_discarded_file = $path.$outfile."_discarded.txt";
$fhout_discarded_file = $path.$outfile."_discarded.gff";
$ostreamReport_file = $path.$outfile."_report.txt";
$fhout_semidDiscarded_file = $path.$outfile."_cannot_be_tested_because_attribute_missing.gff";
}

my $gffout_ok = prepare_gffout($config, $gffout_ok_file);
my $fhout_discarded = prepare_fileout($fhout_discarded_file);
my $fhout_discarded = prepare_gffout($config, $fhout_discarded_file);
my $ostreamReport = prepare_fileout($ostreamReport_file);
my $fhout_semidDiscarded = prepare_gffout($config, $fhout_semidDiscarded_file);

# Manage $primaryTag
my @ptagList;
Expand Down Expand Up @@ -121,17 +124,14 @@
}
}

use Data::Dumper;
print Dumper($value_hash);

# start with some interesting information
my $stringPrint = strftime "%m/%d/%Y at %Hh%Mm%Ss", localtime;
$stringPrint .= "\nusage: $0 @copyARGV\n";
$stringPrint .= "We will discard $print_feature_string that have the attribute $opt_attribute with the value $opt_test $opt_value";
if ($opt_value_insensitive){
$stringPrint .= "case insensitive.\n";
$stringPrint .= " case insensitive.\n";
}else{
$stringPrint .= "case sensitive.\n";
$stringPrint .= " case sensitive.\n";
}

if ($opt_output){
Expand All @@ -142,7 +142,9 @@
#######################
# >>>>>>>>>>>>>>>>>>>>>>>># MAIN #<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
#######################
my %all_cases = ('l1' => 0, 'l2' => 0, 'l3' => 0, 'all' => 0);
my %all_cases = ( 'left' => {'l1' => 0, 'l2' => 0, 'l3' => 0, 'all' => 0},
'discarded' => {'l1' => 0, 'l2' => 0, 'l3' => 0, 'all' => 0} );

######################
### Parse GFF input #
my ($hash_omniscient, $hash_mRNAGeneLink) = slurp_gff3_file_JD({ input => $opt_gff,
Expand All @@ -167,19 +169,29 @@
$removeit = check_feature($feature_l1, 'level1');
# we can remove feature L1 now because we are looping over $hash_sortBySeq not $hash_omniscient
if ($removeit){
my $cases = remove_l1_and_relatives($hash_omniscient, $feature_l1, $fhout_discarded);
$all_cases{'l1'} += $cases->{'l1'};
$all_cases{'l2'} += $cases->{'l2'};
$all_cases{'l3'} += $cases->{'l3'};
$all_cases{'all'} += $cases->{'all'};
my $cases;
if($removeit == 2){
$cases = remove_l1_and_relatives($hash_omniscient, $feature_l1, $fhout_semidDiscarded);
$all_cases{'left'}{'l1'} += $cases->{'l1'};
$all_cases{'left'}{'l2'} += $cases->{'l2'};
$all_cases{'left'}{'l3'} += $cases->{'l3'};
$all_cases{'left'}{'all'} += $cases->{'all'};
} else {
$cases = remove_l1_and_relatives($hash_omniscient, $feature_l1, $fhout_discarded);
$all_cases{'discarded'}{'l1'} += $cases->{'l1'};
$all_cases{'discarded'}{'l2'} += $cases->{'l2'};
$all_cases{'discarded'}{'l3'} += $cases->{'l3'};
$all_cases{'discarded'}{'all'} += $cases->{'all'};
}

next;
}

#################
# == LEVEL 2 == #
#################
my @list_l2_to_remove;
my @list_l3_to_remove;
my %list_l2_to_remove;
my %list_l3_to_remove;
foreach my $tag_l2 (sort keys %{$hash_omniscient->{'level2'}}){ # primary_tag_key_level2 = mrna or mirna or ncrna or trna etc...

if ( exists_keys( $hash_omniscient, ('level2', $tag_l2, $id_l1) ) ){
Expand All @@ -188,7 +200,11 @@

$removeit = check_feature($feature_l2,'level2');
if ($removeit){
push @list_l2_to_remove, [$feature_l2, $tag_l1, $id_l1, $fhout_discarded];
if($removeit == 2){
push ( @{$list_l2_to_remove{'left'}}, [$feature_l2, $tag_l1, $id_l1, $fhout_semidDiscarded]);
} else {
push ( @{$list_l2_to_remove{'discarded'}}, [$feature_l2, $tag_l1, $id_l1, $fhout_discarded]);
}
next;
}
#################
Expand All @@ -203,7 +219,11 @@

$removeit = check_feature($feature_l3, 'level3');
if ($removeit){
push @list_l3_to_remove, [$feature_l3, $tag_l1, $id_l1, $tag_l2, $id_l2, $fhout_discarded];
if($removeit == 2){
push ( @{$list_l3_to_remove{'left'}}, [$feature_l3, $tag_l1, $id_l1, $tag_l2, $id_l2, $fhout_semidDiscarded]);
} else {
push ( @{$list_l3_to_remove{'discarded'}}, [$feature_l3, $tag_l1, $id_l1, $tag_l2, $id_l2, $fhout_discarded]);
}
}
}
}
Expand All @@ -212,22 +232,22 @@
}
}
# Should be removed after looping over them to avoid problems
if (@list_l2_to_remove) {
foreach my $infos (@list_l2_to_remove) {
foreach my $key ( keys %list_l2_to_remove ){
foreach my $infos ( @{$list_l2_to_remove{$key}} ) {
my $cases = remove_l2_and_relatives( $hash_omniscient, @$infos);
$all_cases{'l1'} += $cases->{'l1'};
$all_cases{'l2'} += $cases->{'l2'};
$all_cases{'l3'} += $cases->{'l3'};
$all_cases{'all'} += $cases->{'all'};
$all_cases{$key}{'l1'} += $cases->{'l1'};
$all_cases{$key}{'l2'} += $cases->{'l2'};
$all_cases{$key}{'l3'} += $cases->{'l3'};
$all_cases{$key}{'all'} += $cases->{'all'};
}
}
if (@list_l3_to_remove) {
foreach my $infos (@list_l3_to_remove) {
foreach my $key ( keys %list_l3_to_remove ){
foreach my $infos ( @{$list_l3_to_remove{$key}} ) {
my $cases = remove_l3_and_relatives( $hash_omniscient, @$infos);
$all_cases{'l1'} += $cases->{'l1'};
$all_cases{'l2'} += $cases->{'l2'};
$all_cases{'l3'} += $cases->{'l3'};
$all_cases{'all'} += $cases->{'all'};
$all_cases{$key}{'l1'} += $cases->{'l1'};
$all_cases{$key}{'l2'} += $cases->{'l2'};
$all_cases{$key}{'l3'} += $cases->{'l3'};
$all_cases{$key}{'all'} += $cases->{'all'};
}
}
}
Expand All @@ -236,10 +256,18 @@

print_omniscient( {omniscient => $hash_omniscient, output => $gffout_ok} );

$stringPrint = $all_cases{'all'}." features removed:\n";
$stringPrint .= $all_cases{'l1'}." features level1 (e.g. gene) removed\n";
$stringPrint .= $all_cases{'l2'}." features level2 (e.g. mRNA) removed\n";
$stringPrint .= $all_cases{'l3'}." features level3 (e.g. exon) removed\n";
$stringPrint = "Feature discarded by applying the test (see $fhout_discarded_file file):\n";
$stringPrint .= $all_cases{'discarded'}{'all'}." features removed:\n";
$stringPrint .= $all_cases{'discarded'}{'l1'}." features level1 (e.g. gene) removed\n";
$stringPrint .= $all_cases{'discarded'}{'l2'}." features level2 (e.g. mRNA) removed\n";
$stringPrint .= $all_cases{'discarded'}{'l3'}." features level3 (e.g. exon) removed\n";

$stringPrint .= "Feature left out because the attribute is missing (see $fhout_semidDiscarded_file file):\n";
$stringPrint .= $all_cases{'left'}{'all'}." features removed:\n";
$stringPrint .= $all_cases{'left'}{'l1'}." features level1 (e.g. gene) removed\n";
$stringPrint .= $all_cases{'left'}{'l2'}." features level2 (e.g. mRNA) removed\n";
$stringPrint .= $all_cases{'left'}{'l3'}." features level3 (e.g. exon) removed\n";

if ($opt_output){
print $ostreamReport $stringPrint;
print $stringPrint;
Expand Down Expand Up @@ -298,35 +326,45 @@ sub should_we_remove_feature{
}
# for string values replace = by eq and ! by ne and avoid other type of test
if ( ! looks_like_number ($given_value) or ! looks_like_number ($file_value)){
print "String case\n" if $opt_verbose;
if ($opt_test eq "="){
if ($file_value eq $given_value){return 1; }
if ($file_value eq $given_value) { print "equal\n" if $opt_verbose; return 1; }
else { print "not equal\n" if $opt_verbose; }
}
elsif ($opt_test eq "!"){
if ($file_value ne $given_value){return 1; }
if ($file_value ne $given_value){ print "different\n" if $opt_verbose; return 1; }
else { print "not different\n" if $opt_verbose; }
}
}
else{
print "Number case\n" if $opt_verbose;
if ($opt_test eq "="){
if ($file_value == $given_value){return 1; }
}
elsif ($opt_test eq "!"){
if ($file_value != $given_value){return 1; }
}
elsif ($opt_test eq ">"){
if ($file_value > $given_value){return 1; }
}
elsif ($opt_test eq "<"){
if ($file_value < $given_value){return 1; }
}
elsif ($opt_test eq "<="){
if ($file_value <= $given_value){return 1; }
}
elsif ($opt_test eq ">="){
if ($file_value >= $given_value){return 1; }
}
}
elsif ($opt_test eq "="){
if ($file_value == $given_value){return 1; }
}
elsif ($opt_test eq "!"){
if ($file_value != $given_value){return 1; }
}
elsif ($opt_test eq ">"){
if ($file_value > $given_value){return 1; }
}
elsif ($opt_test eq "<"){
if ($file_value < $given_value){return 1; }
}
elsif ($opt_test eq "<="){
if ($file_value <= $given_value){return 1; }
}
elsif ($opt_test eq ">="){
if ($file_value >= $given_value){return 1; }
}
}
}
return 0;
} else {
print "Attribute not found case\n" if $opt_verbose;
print "$opt_attribute ".$feature->gff_string."\n";
return 2;
}
return 0;
}

__END__
Expand Down

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