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sort tag L2 #487

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Sep 9, 2024
Merged

sort tag L2 #487

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72 changes: 36 additions & 36 deletions lib/AGAT/OmniscientO.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -398,62 +398,62 @@ sub print_omniscient_from_level1_id_list {
if( defined($args->{output})) {$gffout = $args->{output};} else{ print "Output parameter mandatory to use print_omniscient_from_level1_id_list!"; exit; }
# -----------------------------------

#uri_decode_omniscient($omniscient);
#uri_decode_omniscient($omniscient);

# --------- deal with header --------------
write_headers($omniscient, $gffout);
# --------- deal with header --------------
write_headers($omniscient, $gffout);

# sort by seq id
# sort by seq id
my ( $hash_sortBySeq, $hash_sortBySeq_std, $hash_sortBySeq_topf ) = collect_l1_info_sorted_by_seqid_and_location($omniscient, $level_id_list);

#Read by seqId to sort properly the output by seq ID
foreach my $seqid ( sort { ncmp ($a, $b) } keys %{$hash_sortBySeq}){ # loop over all the feature level1
#Read by seqId to sort properly the output by seq ID
foreach my $seqid ( sort { ncmp ($a, $b) } keys %{$hash_sortBySeq}){ # loop over all the feature level1

#################
# == LEVEL 1 == #
#################
#################
# == LEVEL 1 == #
#################
write_top_features($gffout, $seqid, $hash_sortBySeq_topf, $omniscient);

foreach my $locationid ( sort { ncmp ($a, $b) } keys %{$hash_sortBySeq->{$seqid} } ){

my $primary_tag_l1 = $hash_sortBySeq->{$seqid}{$locationid}{'tag'};
my $id_tag_key_level1 = $hash_sortBySeq->{$seqid}{$locationid}{'id'};

#_uri_encode_one_feature($omniscient->{'level1'}{$primary_tag_l1}{$id_tag_key_level1});
#_uri_encode_one_feature($omniscient->{'level1'}{$primary_tag_l1}{$id_tag_key_level1});

$gffout->write_feature($omniscient->{'level1'}{$primary_tag_l1}{$id_tag_key_level1}); # print feature
$gffout->write_feature($omniscient->{'level1'}{$primary_tag_l1}{$id_tag_key_level1}); # print feature

#################
# == LEVEL 2 == #
#################
foreach my $primary_tag_key_level2 (keys %{$omniscient->{'level2'}}){ # primary_tag_key_level2 = mrna or mirna or ncrna or trna etc...
#################
# == LEVEL 2 == #
#################
foreach my $primary_tag_key_level2 ( sort {$a cmp $b} keys %{$omniscient->{'level2'}}){ # primary_tag_key_level2 = mrna or mirna or ncrna or trna etc...

if ( exists ($omniscient->{'level2'}{$primary_tag_key_level2}{$id_tag_key_level1} ) ){
foreach my $feature_level2 ( sort { ncmp ($a->start."|".$a->end.$a->_tag_value('ID'), $b->start."|".$b->end.$b->_tag_value('ID') ) } @{$omniscient->{'level2'}{$primary_tag_key_level2}{$id_tag_key_level1}}) {
if ( exists ($omniscient->{'level2'}{$primary_tag_key_level2}{$id_tag_key_level1} ) ){
foreach my $feature_level2 ( sort { ncmp ($a->start."|".$a->end.$a->_tag_value('ID'), $b->start."|".$b->end.$b->_tag_value('ID') ) } @{$omniscient->{'level2'}{$primary_tag_key_level2}{$id_tag_key_level1}}) {

#_uri_encode_one_feature($feature_level2);
#_uri_encode_one_feature($feature_level2);

$gffout->write_feature($feature_level2);
$gffout->write_feature($feature_level2);

#################
# == LEVEL 3 == #
#################
my $level2_ID ;
if($feature_level2->has_tag('ID')){
$level2_ID = lc($feature_level2->_tag_value('ID'));
}
elsif($feature_level2->has_tag('transcript_id')){
$level2_ID = lc( $feature_level2->_tag_value('transcript_id'));
}
else{
warn "Cannot retrieve the parent feature of the following feature: ".gff_string($feature_level2);
}
#################
# == LEVEL 3 == #
#################
my $level2_ID ;
if($feature_level2->has_tag('ID')){
$level2_ID = lc($feature_level2->_tag_value('ID'));
}
elsif($feature_level2->has_tag('transcript_id')){
$level2_ID = lc( $feature_level2->_tag_value('transcript_id'));
}
else{
warn "Cannot retrieve the parent feature of the following feature: ".gff_string($feature_level2);
}

print_level3_old_school( {omniscient => $omniscient, level2_ID =>$level2_ID, output => $gffout} );
print_level3_old_school( {omniscient => $omniscient, level2_ID =>$level2_ID, output => $gffout} );

}
}
}
}
}
}
}
}

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