agat_sp_complement_annotations.pl does not complement but concatenate?

[dirkjanvw]

Describe the bug
I would like to complement one GFF file with those non-overlapping genes from another GFF file. From the documentation it seems agat_sp_complement_annotations.pl is meant for this. However, when I run it, it concatenates instead of complementing.

General (please complete the following information):

• AGAT version: v1.2.0
• AGAT installation/use: bioconda
• OS: Ubuntu

To Reproduce
ref.gff:

Chr1	Helixer	gene	41064	54753	.	+	.	ID=Chr1_000001
Chr1	Helixer	mRNA	41064	54753	.	+	.	ID=Chr1_000001.1;Parent=Chr1_000001
Chr1	Helixer	exon	41064	54753	.	+	.	ID=Chr1_000001.1.exon.1;Parent=Chr1_000001.1
Chr1	Helixer	five_prime_UTR	41064	41310	.	+	.	ID=Chr1_000001.1.five_prime_UTR.1;Parent=Chr1_000001.1
Chr1	Helixer	CDS	41311	54435	.	+	0	ID=Chr1_000001.1.CDS.1;Parent=Chr1_000001.1
Chr1	Helixer	three_prime_UTR	54436	54753	.	+	.	ID=Chr1_000001.1.three_prime_UTR.1;Parent=Chr1_000001.1

add.gff:

Chr1	Liftoff	gene	41075	54676	.	+	.	ID=gene-gene1
Chr1	Liftoff	mRNA	41075	54676	.	+	.	ID=rna-transcript1;Parent=gene-gene1
Chr1	Liftoff	exon	41075	54676	.	+	.	ID=exon-transcript1-1;Parent=rna-transcript1
Chr1	Liftoff	CDS	41311	54435	.	+	0	ID=cds-codingsequence-1.1;Parent=rna-transcript1
Chr1	Liftoff	five_prime_UTR	41075	41310	.	+	.	ID=nbis-five_prime_utr-19342;Parent=rna-transcript1
Chr1	Liftoff	three_prime_UTR	54436	54676	.	+	.	ID=nbis-three_prime_utr-18368;Parent=rna-transcript1

Running AGAT as:

agat_sp_complement_annotations.pl --ref ref.gff --add add.gff

Expected behavior
I expected the resulting gff file to only contain the reference record instead of both.

Screenshots
This is what the output of AGAT looks like instead:

Additional context
NA

[Juke34]

Hi,

Thank you for using AGAT and reporting this issue.
This is indeed a bug I think Introduced quite recently. It push a fix soon.

Best regards,
/Jacques

[dirkjanvw]

Thanks a lot for the fast fix! When do you plan on making a new release so I can easily install it via bioconda? For testing it I can create a custom singularity image but I think a new release would be easier :)

[dirkjanvw]

I tried creating the custom singularity image by following the manual installation instructions in the README, but I failed:

Bootstrap: docker
From: r-base:4.3.2

%post
   apt-get update
   apt-get install -y git
   apt-get install -y libbio-perl-perl libclone-perl libgraph-perl liblwp-useragent-determined-perl libstatistics-r-perl libcarp-clan-perl libsort-naturally-perl libfile-share-perl libfile-sharedir-install-perl libyaml-perl liblwp-protocol-https-perl libstatistics-r-perl

%post
   apt-get install -y perl-modules cpanminus
   cpanm Bio::DB::Fasta Bio::DB::Taxonomy Bio::OntologyIO::obo Bio::Ontology::OntologyEngineI Bio::Seq Bio::SeqIO Bio::Tools::CodonTable Bio::Tools::GFF Carp Clone Cwd Exporter File::Basename File::Copy File::Share Getopt::Long IO::File IPC::Open2 YAML LWP::UserAgent LWP::Protocol::https List::MoreUtils Moose POSIX Pod::Usage Scalar::Util Sort::Naturally Term::ProgressBar Time::Piece Time::Seconds Try::Tiny URI::Escape

%post
   cd /opt
   git clone https://github.com/NBISweden/AGAT.git
   cd AGAT
   git checkout  180374e
   perl Makefile.PL
   make
   make test
   make install

%environment
   export PERL5LIB="/opt/AGAT/blib/lib/:$PERL5LIB"

It fails at make test, but when I leave out make test it also fails because:

Undefined subroutine &main::prepare_gffout called at /usr/local/bin/agat_sp_complement_annotations.pl line 55.

[Juke34]

I do not know if I will have time to make release soon.
Why do you use a r-base image in your container? Maybe you will have better chance with an simple ubuntu OS.
Otherwise what you can do is to install the last version via conda, activate the env then run

git clone https://github.com/NBISweden/AGAT.git
cd AGAT
perl Makefile.PL
make
make test
make install

[dirkjanvw]

I thought the r-base would be the best choice since R is needed for some plots, but I also tested a perl base and it doesn't work either.

Anyway, with the conda install it works! I'll use that for now.