add test for param deflate_attribute

NBISweden · Dec 3, 2024 · 2a8ef72 · 2a8ef72
1 parent a9168e6
commit 2a8ef72
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Showing 5 changed files with 27 additions and 4 deletions.
diff --git a/t/config.t b/t/config.t
@@ -40,6 +40,7 @@ system("$script config -e \\
 								--gff_output_version 2  \\
 								--gtf_output_version 2  \\
 								--debug  \\
+								--deflate_attribute  \\
 								--no-check_all_level1_locations  \\
 								--no-check_identical_isoforms  \\
 								--no-check_utrs  \\

diff --git a/t/config/out/agat_config.yaml b/t/config/out/agat_config.yaml
@@ -12,6 +12,7 @@ check_utrs: false
 clean_attributes_from_template: true
 create_l3_for_l2_orphan: false
 debug: true
+deflate_attribute: true
 force_gff_input_version: 3
 gff_output_version: 2
 gtf_output_version: 2

diff --git a/t/gff_other.t b/t/gff_other.t
@@ -2,7 +2,7 @@
 
 use strict;
 use warnings;
-use Test::More tests => 8;
+use Test::More tests => 9;
 
 =head1 DESCRIPTION
 
@@ -101,13 +101,25 @@ $correct_output = "$output_folder/issue448.gtf";
 system("$script_agat config --expose --output_format gtf 2>&1 1>/dev/null");
 system("$script --g $input_folder/issue448.gtf -o $pathtmp  2>&1 1>/dev/null");
 
-ok( system("diff $pathtmp $correct_output") == 0, "issue441 check");
+ok( system("diff $pathtmp $correct_output") == 0, "issue448 check");
 
 unlink $pathtmp;
 unlink $config;
 
 $correct_output = "$output_folder/issue448.gff";
 system("$script --g $input_folder/issue448.gtf -o $pathtmp  2>&1 1>/dev/null");
 
-ok( system("diff $pathtmp $correct_output") == 0, "issue441 check");
-unlink $pathtmp;
+ok( system("diff $pathtmp $correct_output") == 0, "issue448 check");
+unlink $pathtmp;
+
+# --------- Issue 457 multi-values attributes (gene_name "26266" "MT-TL1";) can be deflated to be compliant with GTF and CellRanger
+
+$script = $script_prefix."bin/agat_convert_sp_gff2gtf.pl";
+$correct_output = "$output_folder/issue457.gtf";
+
+system("$script_agat config --expose --deflate_attribute 2>&1 1>/dev/null");
+system("$script --gff $input_folder/issue457.gff -o $pathtmp  2>&1 1>/dev/null");
+
+ok( system("diff $pathtmp $correct_output") == 0, "issue457 check");
+unlink $pathtmp;
+unlink $config;
diff --git a/t/gff_other/in/issue457.gff b/t/gff_other/in/issue457.gff
@@ -0,0 +1,4 @@
+##gff-version 3
+chrM	AGAT	gene	3230	3304	.	+	.	ID=agat-gene-1;gene_id=26266;gene_name=26266,MT-TL1;gene_type=misc_RNA;hgnc_id=HGNC:7490;level=3;merged_ID=ENSG00000209082.1;merged_gene_id=ENSG00000209082.1,26266;tag=basic,Ensembl_canonical;transcript_name=26266,MT-TL1-201;transcript_support_level=NA;transcript_type=misc_RNA
+chrM	ENSEMBL	transcript	3230	3304	.	+	.	ID=26266;Parent=agat-gene-1;gene_id=26266;gene_name=26266;gene_type=misc_RNA;level=3;merged_ID=ENST00000386347.1;merged_Parent=ENSG00000209082.1;merged_gene_id=ENSG00000209082.1,26266;merged_gene_name=MT-TL1,26266;merged_gene_type=misc_RNA;merged_hgnc_id=HGNC:7490;merged_level=3;merged_tag=basic,Ensembl_canonical;merged_transcript_id=ENST00000386347.1,26266;merged_transcript_name=MT-TL1-201,26266;merged_transcript_support_level=NA;merged_transcript_type=misc_RNA;transcript_id=26266;transcript_name=26266;transcript_type=misc_RNA
+chrM	ENSEMBL	exon	3230	3304	.	+	.	ID=agat-exon-1;Parent=26266;gene_id=26266;gene_name=26266;gene_type=misc_RNA;level=3;transcript_id=26266;transcript_name=26266;transcript_type=misc_RNA
diff --git a/t/gff_other/out/issue457.gtf b/t/gff_other/out/issue457.gtf
@@ -0,0 +1,5 @@
+##gtf-version X
+# GFF-like GTF i.e. not checked against any GTF specification. Conversion based on GFF input, standardised by AGAT.
+chrM	AGAT	gene	3230	3304	.	+	.	gene_id "26266"; ID "agat-gene-1"; gene_name "26266"; gene_name_1 "MT-TL1"; gene_type "misc_RNA"; hgnc_id "HGNC:7490"; level "3"; merged_ID "ENSG00000209082.1"; merged_gene_id "ENSG00000209082.1"; merged_gene_id_1 "26266"; tag "basic"; tag_1 "Ensembl_canonical"; transcript_name "26266"; transcript_name_1 "MT-TL1-201"; transcript_support_level "NA"; transcript_type "misc_RNA";
+chrM	ENSEMBL	transcript	3230	3304	.	+	.	gene_id "26266"; transcript_id "26266"; ID "26266"; Parent "agat-gene-1"; gene_name "26266"; gene_type "misc_RNA"; level "3"; merged_ID "ENST00000386347.1"; merged_Parent "ENSG00000209082.1"; merged_gene_id "ENSG00000209082.1"; merged_gene_id_1 "26266"; merged_gene_name "MT-TL1"; merged_gene_name_1 "26266"; merged_gene_type "misc_RNA"; merged_hgnc_id "HGNC:7490"; merged_level "3"; merged_tag "basic"; merged_tag_1 "Ensembl_canonical"; merged_transcript_id "ENST00000386347.1"; merged_transcript_id_1 "26266"; merged_transcript_name "MT-TL1-201"; merged_transcript_name_1 "26266"; merged_transcript_support_level "NA"; merged_transcript_type "misc_RNA"; transcript_name "26266"; transcript_type "misc_RNA";
+chrM	ENSEMBL	exon	3230	3304	.	+	.	gene_id "26266"; transcript_id "26266"; ID "agat-exon-1"; Parent "26266"; gene_name "26266"; gene_type "misc_RNA"; level "3"; transcript_name "26266"; transcript_type "misc_RNA";