From a23b8ea5622d390e3b71316788c5b4d11af0eb03 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Wed, 27 Mar 2024 22:23:36 +0100 Subject: [PATCH] =?UTF-8?q?Fix=20445=20buggit=20add=20=20lib/AGAT/Omniscie?= =?UTF-8?q?ntI.pm=20Few=20gene=20in=20output=20due=20to=E2=80=A6=20(#447)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Fix 445 bug introduced in version 1.3.2 in lib/AGAT/OmniscientI.pm : Few gene in output due to a remaining last that quit early in a loop. remove useless print * increment version --- lib/AGAT/AGAT.pm | 2 +- lib/AGAT/OmniscientI.pm | 5 ----- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/lib/AGAT/AGAT.pm b/lib/AGAT/AGAT.pm index 6e7a18bf..7a48d14c 100644 --- a/lib/AGAT/AGAT.pm +++ b/lib/AGAT/AGAT.pm @@ -16,7 +16,7 @@ use AGAT::Utilities; use AGAT::PlotR; use Bio::Tools::GFF; -our $VERSION = "v1.3.2"; +our $VERSION = "v1.3.3"; our @ISA = qw(Exporter); our @EXPORT = qw(get_agat_header print_agat_version get_agat_config handle_levels); sub import { diff --git a/lib/AGAT/OmniscientI.pm b/lib/AGAT/OmniscientI.pm index 3b81e951..4a6f68e5 100644 --- a/lib/AGAT/OmniscientI.pm +++ b/lib/AGAT/OmniscientI.pm @@ -1731,18 +1731,14 @@ sub _check_l2_linked_to_l3{ #check if we have the tag foreach my $l3_feature (@{$hash_omniscient->{'level3'}{$tag_l3}{$id_l2}}){ - print "fefe ".$l3_feature->gff_string()."\n"; if($l3_feature->has_tag($tag) ) { - print "has_tag $tag\n"; # case where it's linked by comon_tag attribute if (exists_keys($common_tag_in_l1,( $tag, lc($l3_feature->_tag_value($tag)) ) ) ){ - print "exists_keys\n"; if($#{$common_tag_in_l1->{$tag}{lc($l3_feature->_tag_value($tag))}} == 0){ my $id = $common_tag_in_l1->{$tag}{lc($l3_feature->_tag_value($tag))}[0]->{'id'}; my $ptag = $common_tag_in_l1->{$tag}{lc($l3_feature->_tag_value($tag))}[0]->{'ptag'}; $has_l1_feature = $hash_omniscient->{'level1'}{$ptag}{$id}; $id_l2_to_replace = $l3_feature->_tag_value('Parent'); - print "goes into it !!!! $id_l2_to_replace \n"; last; } else{ @@ -1827,7 +1823,6 @@ sub _check_l2_linked_to_l3{ push(@{$hash_omniscient->{"level2"}{lc($l2_feature->primary_tag)}{lc($l1_ID)}}, $l2_feature); } dual_print($log, "L3 had a L1 feature but no L2 feature. Corrected by creating the intermediate L2 feature:\n".$l2_feature->gff_string()."\nUsing this feature template:\n".$hash_omniscient->{"level3"}{$tag_l3}{$id_l2}[0]->gff_string()."\n", $verbose); - last }