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new agat_sp_flag_short_introns.pl script to flag a record when an int…
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…ron is shorten than expected value with the short_intron attribute
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@Juke34
Juke34 committed Jan 7, 2025
1 parent 1217a04 commit 6812637
Showing 1 changed file with 26 additions and 88 deletions.
114 changes: 26 additions & 88 deletions bin/agat_sp_flag_short_introns.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,11 @@

my @copyARGV=@ARGV;
if ( !GetOptions( 'f|gff|ref|reffile=s' => \$opt_file,
'o|out|output=s' => \$opt_output,
'v|verbose!' => \$verbose,
'i|intron_size=i' => \$Xsize,
'c|config=s' => \$config,
'h|help!' => \$opt_help ) )
'o|out|output=s' => \$opt_output,
'v|verbose!' => \$verbose,
'i|intron_size=i' => \$Xsize,
'c|config=s' => \$config,
'h|help!' => \$opt_help ) )
{
pod2usage( { -message => 'Failed to parse command line',
-verbose => 1,
Expand Down Expand Up @@ -82,82 +82,31 @@
#########################

my $nb_cases=0;
my $tag = "pseudo";
my $tag = "short_intron";
######################
### Parse GFF input #
foreach my $tag_l1 (keys %{$hash_omniscient->{'level1'}}){
foreach my $id_l1 (keys %{$hash_omniscient->{'level1'}{$tag_l1}}){
my $shortest_intron=10000000000;
foreach my $tag_l2 (keys %{$hash_omniscient->{'level2'}}){
if (exists_keys($hash_omniscient,('level2',$tag_l2,$id_l1) ) ){
# #MATCH CASE - We ahve to count the L2 match features
# if($tag_l2 =~ "match"){
# my $counterL2_match=-1;
# foreach my $feature_l2 (@{$hash_omniscient->{'level2'}{$tag_l2}{$id_l1}}){

# my @sortedList = sort {$a->start <=> $b->start} @{$hash_omniscient->{'level2'}{$tag_l2}{$id_l1}};
# my $indexLastL2 = $#{$hash_omniscient->{'level2'}{$tag_l2}{$id_l1}};
# $counterL2_match++;

# if($counterL2_match > 0 and $counterL2_match <= $indexLastL2){
# my $intronSize = $sortedList[$counterL2_match]->start - $sortedList[$counterL2_match-1]->end;
# $shortest_intron = $intronSize if($intronSize < $shortest_intron)
# }
# }
# }
# else{
foreach my $feature_l2 (@{$hash_omniscient->{'level2'}{$tag_l2}{$id_l1}}){
my $level2_ID = lc($feature_l2->_tag_value('ID'));

# if ( exists_keys($hash_omniscient,('level3','exon',$level2_ID) ) ){
# my $counterL3=-1;
# my $indexLast = $#{$hash_omniscient->{'level3'}{'exon'}{$level2_ID}};
# my @sortedList = sort {$a->start <=> $b->start} @{$hash_omniscient->{'level3'}{'exon'}{$level2_ID}};
# foreach my $feature_l3 ( @sortedList ){
# #count number feature of tag_l3 type
# $counterL3++;
# #Manage Introns## from the second intron to the last (from index 1 to last index of the table sortedList) ## We go inside this loop only if we have more than 1 feature.
# if($counterL3 > 0 and $counterL3 <= $indexLast){
# my $intronSize = $sortedList[$counterL3]->start - $sortedList[$counterL3-1]->end;
# $shortest_intron = $intronSize if($intronSize < $shortest_intron)
# }
# }
# }
# else{
if ( exists_keys($hash_omniscient,('level3','cds',$level2_ID)) ){
my $counterL3=-1;
my $indexLast = $#{$hash_omniscient->{'level3'}{'cds'}{$level2_ID}};
my @sortedList = sort {$a->start <=> $b->start} @{$hash_omniscient->{'level3'}{'cds'}{$level2_ID}};
foreach my $feature_l3 ( @sortedList ){
#count number feature of tag_l3 type
$counterL3++;
#Manage Introns## from the second intron to the last (from index 1 to last index of the table sortedList) ## We go inside this loop only if we have more than 1 feature.
if($counterL3 > 0 and $counterL3 <= $indexLast){
my $intronSize = $sortedList[$counterL3]->start - $sortedList[$counterL3-1]->end;
$shortest_intron = $intronSize if($intronSize < $shortest_intron)
}
}
foreach my $feature_l2 (@{$hash_omniscient->{'level2'}{$tag_l2}{$id_l1}}){
my $level2_ID = lc($feature_l2->_tag_value('ID'));

if ( exists_keys($hash_omniscient,('level3', 'exon', $level2_ID)) ){
my $counterL3=-1;
my $indexLast = $#{$hash_omniscient->{'level3'}{'exon'}{$level2_ID}};
my @sortedList = sort {$a->start <=> $b->start} @{$hash_omniscient->{'level3'}{'exon'}{$level2_ID}};
foreach my $feature_l3 ( @sortedList ){
#count number feature of tag_l3 type
$counterL3++;
#Manage Introns## from the second intron to the last (from index 1 to last index of the table sortedList) ## We go inside this loop only if we have more than 1 feature.
if($counterL3 > 0 and $counterL3 <= $indexLast){
my $intronSize = $sortedList[$counterL3]->start - $sortedList[$counterL3-1]->end;
$shortest_intron = $intronSize if($intronSize < $shortest_intron)
}
# foreach my $tag_l3 (keys %{$hash_omniscient->{'level3'}}){
# if (index(lc($tag_l3), 'utr') != -1) {
# if ( exists_keys($hash_omniscient,('level3',$tag_l3,$level2_ID)) ){
# my $counterL3=-1;
# my $indexLast = $#{$hash_omniscient->{'level3'}{$tag_l3}{$level2_ID}};
# my @sortedList = sort {$a->start <=> $b->start} @{$hash_omniscient->{'level3'}{$tag_l3}{$level2_ID}};
# foreach my $feature_l3 ( @sortedList ){
# #count number feature of tag_l3 type
# $counterL3++;
# #Manage Introns## from the second intron to the last (from index 1 to last index of the table sortedList) ## We go inside this loop only if we have more than 1 feature.
# if($counterL3 > 0 and $counterL3 <= $indexLast){
# my $intronSize = $sortedList[$counterL3]->start - $sortedList[$counterL3-1]->end;
# $shortest_intron = $intronSize if($intronSize < $shortest_intron)
# }
# }
# }
# }
# }
#}
#}
}
}
}
}
}
Expand All @@ -168,28 +117,17 @@

my $feature_l1 = $hash_omniscient->{'level1'}{$tag_l1}{$id_l1};
$feature_l1->add_tag_value($tag, $shortest_intron);
if($feature_l1->has_tag('product') ){
$feature_l1->add_tag_value('note', $feature_l1->get_tag_values('product'));
$feature_l1->remove_tag('product');
}

foreach my $tag_l2 (keys %{$hash_omniscient->{'level2'}}){
if (exists_keys ($hash_omniscient, ('level2', $tag_l2, $id_l1) ) ) {
foreach my $feature_l2 (@{$hash_omniscient->{'level2'}{$tag_l2}{$id_l1}}){
my $level2_ID = lc($feature_l2->_tag_value('ID'));
$feature_l2->add_tag_value($tag, $shortest_intron);
if($feature_l2->has_tag('product') ){
$feature_l2->add_tag_value('note', $feature_l2->get_tag_values('product'));
$feature_l2->remove_tag('product');
}

foreach my $tag_l3 (keys %{$hash_omniscient->{'level3'}}){
if ( exists_keys($hash_omniscient, ('level3', $tag_l3, $level2_ID) ) ){
foreach my $feature_l3 (@{$hash_omniscient->{'level3'}{$tag_l3}{$level2_ID}}){
$feature_l3->add_tag_value($tag, $shortest_intron);
if($feature_l3->has_tag('product') ){
$feature_l3->add_tag_value('note', $feature_l3->get_tag_values('product'));
$feature_l3->remove_tag('product');
}
}
}
}
Expand Down Expand Up @@ -234,9 +172,9 @@ =head1 NAME
=head1 DESCRIPTION
The script flags the short introns with the attribute <pseudo>.
Is is usefull to avoid ERROR when submiting the data to EBI.
(Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy)
Looking at exon features the script flags each feature of a record with the <short_intron> attribute if
it contains an intron with a size below the <--intron_size> threshold (10bp by default).
The value of this attribute will be the size of the shortest intron found under the threshold.
=head1 SYNOPSIS
Expand Down

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