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add na_aside parameter for cases where the attribute tag is missing
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@Juke34
Juke34 committed Jul 9, 2024
1 parent 33f5333 commit 38ca498
Showing 1 changed file with 50 additions and 33 deletions.
83 changes: 50 additions & 33 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 @@ -15,6 +15,8 @@
my $primaryTag=undef;
my $opt_output= undef;
my $opt_value = undef;
my $opt_keep_parental = undef;
my $opt_na_aside = undef;
my $opt_value_insensitive = undef;
my $opt_attribute = undef;
my $opt_test = "=";
Expand All @@ -27,6 +29,8 @@
if ( !GetOptions( 'f|ref|reffile|gff=s' => \$opt_gff,
'value=s' => \$opt_value,
'value_insensitive!' => \$opt_value_insensitive,
'keep_parental!' => \$opt_keep_parental,
'na_aside!' => \$opt_na_aside,
"p|type|l=s" => \$primaryTag,
'a|attribute=s' => \$opt_attribute,
't|test=s' => \$opt_test,
Expand Down Expand Up @@ -70,7 +74,7 @@
my $gffout_ok_file ;
my $fhout_discarded_file ;
my $ostreamReport_file;
my $fhout_semidDiscarded_file;
my $fhout_semidDiscarded_file if $opt_na_aside;

if ($opt_output) {
my ($outfile,$path,$ext) = fileparse($opt_output,qr/\.[^.]*/);
Expand All @@ -79,13 +83,13 @@
$gffout_ok_file = $path.$outfile.$ext;
$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";
$fhout_semidDiscarded_file = $path.$outfile."_na.gff";
}

my $gffout_ok = prepare_gffout($config, $gffout_ok_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);
my $fhout_semidDiscarded = prepare_gffout($config, $fhout_semidDiscarded_file) if $opt_na_aside;

# Manage $primaryTag
my @ptagList;
Expand Down Expand Up @@ -170,20 +174,19 @@
# we can remove feature L1 now because we are looping over $hash_sortBySeq not $hash_omniscient
if ($removeit){
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'} += $cases->{'all'};
} else {
if($removeit == 1){
$cases = remove_l1_and_relatives($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'} += $cases->{'all'};
} elsif ($removeit == 2 and $opt_na_aside){
$cases = remove_l1_and_relatives($hash_omniscient, $feature_l1, $fhout_semidDiscarded);
$all_cases{'na'}{'l1'} += $cases->{'l1'};
$all_cases{'na'}{'l2'} += $cases->{'l2'};
$all_cases{'na'}{'l3'} += $cases->{'l3'};
$all_cases{'na'}{'all'} += $cases->{'all'};
}

next;
}

Expand All @@ -200,10 +203,10 @@

$removeit = check_feature($feature_l2,'level2');
if ($removeit){
if($removeit == 2){
push ( @{$list_l2_to_remove{'left'}}, [$feature_l2, $tag_l1, $id_l1, $fhout_semidDiscarded]);
} else {
if ($removeit == 1){
push ( @{$list_l2_to_remove{'discarded'}}, [$feature_l2, $tag_l1, $id_l1, $fhout_discarded]);
} elsif ($removeit == 2 and $opt_na_aside){
push ( @{$list_l2_to_remove{'na'}}, [$feature_l2, $tag_l1, $id_l1, $fhout_semidDiscarded]);
}
next;
}
Expand All @@ -218,12 +221,10 @@
foreach my $feature_l3 ( @list_fl3 ) {

$removeit = check_feature($feature_l3, 'level3');
if ($removeit){
if($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, $fhout_discarded]);
}
if($removeit == 1){
push ( @{$list_l3_to_remove{'discarded'}}, [$feature_l3, $tag_l1, $id_l1, $tag_l2, $id_l2, $fhout_discarded]);
} elsif ( $removeit == 2 and $opt_na_aside ){
push ( @{$list_l3_to_remove{'na'}}, [$feature_l3, $tag_l1, $id_l1, $tag_l2, $id_l2, $fhout_semidDiscarded]);
}
}
}
Expand All @@ -234,16 +235,16 @@
# Should be removed after looping over them to avoid problems
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);
my $cases = remove_l2_and_relatives( $hash_omniscient, @$infos, $opt_keep_parental);
$all_cases{$key}{'l1'} += $cases->{'l1'};
$all_cases{$key}{'l2'} += $cases->{'l2'};
$all_cases{$key}{'l3'} += $cases->{'l3'};
$all_cases{$key}{'all'} += $cases->{'all'};
}
}
foreach my $key ( keys %list_l3_to_remove ){
foreach my $key ( sort keys %list_l3_to_remove ){
foreach my $infos ( @{$list_l3_to_remove{$key}} ) {
my $cases = remove_l3_and_relatives( $hash_omniscient, @$infos);
my $cases = remove_l3_and_relatives( $hash_omniscient, @$infos, $opt_keep_parental);
$all_cases{$key}{'l1'} += $cases->{'l1'};
$all_cases{$key}{'l2'} += $cases->{'l2'};
$all_cases{$key}{'l3'} += $cases->{'l3'};
Expand All @@ -262,11 +263,13 @@
$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_na_aside){
$stringPrint .= "Feature left out because the attribute is missing (see $fhout_semidDiscarded_file file):\n";
$stringPrint .= $all_cases{'na'}{'all'}." features removed:\n";
$stringPrint .= $all_cases{'na'}{'l1'}." features level1 (e.g. gene) removed\n";
$stringPrint .= $all_cases{'na'}{'l2'}." features level2 (e.g. mRNA) removed\n";
$stringPrint .= $all_cases{'na'}{'l3'}." features level3 (e.g. exon) removed\n";
}

if ($opt_output){
print $ostreamReport $stringPrint;
Expand Down Expand Up @@ -362,7 +365,6 @@ sub should_we_remove_feature{
return 0;
} else {
print "Attribute not found case\n" if $opt_verbose;
print "$opt_attribute ".$feature->gff_string."\n";
return 2;
}
}
Expand All @@ -376,11 +378,16 @@ =head1 NAME
=head1 DESCRIPTION
The script aims to filter features according to attribute value (9th column).
If the attribute tag is missing the feature will not be discarded.
If the attribute exists and the value pass the test, the feature is discarded.
- If the attribute exists and the value do not pass the test, the feature is written into <output>.
- If the attribute exists and the value pass the test, the feature is discarded and written into <output>_discarded.gff.
- If the attribute tag is missing (test cannot be applyed), the feature will be written into <output> by default. If --na_aside parameter
is activated then it will be written into <output>_na.gff.
Attribute are stored in the 9th column and have this shape: tag=value
/!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures, and
removing all children of a feature will automatically remove this feature too.
/!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures.
/!\ Removing all children of a feature will automatically remove this feature too (excepted if --keep_parental is activated).
/!\ If --keep_parental is not activated and --na_aside is activated, and all level3 features of a record are split between both <output>_na.gff and <output>_discarded.gff,
, then the parental level1 and level2 features are removed and will end up in the <output>_na.gff file only.
=head1 SYNOPSIS
Expand Down Expand Up @@ -416,6 +423,16 @@ =head1 OPTIONS
Bolean. Deactivated by default. When activated the values provided by the --value parameter are handled case insensitive.
=item B<--na_aside>
Bolean. Deactivated by default. By default if the attribute tag on which the filter is based is missing, the feature will be written into <output>.
When activated, such features will be written into a separate file called <output>_na.gff
=item B<--keep_parental>
Bolean. Deactivated by default. When activated even if all child features have been removed, the parental one will be kept.
=item B<-t> or B<--test>
Test to apply (> < = ! >= <=). default value "=".
If you use one of these two character >, <, please don't forget to quote the
Expand Down

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