viash-hub · rcannood · Oct 26, 2024 · Jul 31, 2024 · Jul 31, 2024 · Jul 31, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,10 @@
 
 * `nanoplot`: Plotting tool for long read sequencing data and alignments (PR #95).
 
+* `agat`:
+  - `agat/agat_sp_add_introns`: add intron features to gtf/gff file without intron features (PR #104).
+
+
 ## BREAKING CHANGES
 
 * `falco`: Fix a typo in the `--reverse_complement` argument (PR #157).
@@ -55,6 +59,7 @@
   - `agat/agat_convert_sp_gff2tsv`: convert gtf/gff file into tabulated file (PR #102).
   - `agat/agat_convert_sp_gxf2gxf`: fixes and/or standardizes any GTF/GFF file into full sorted GTF/GFF file (PR #103).
 
+
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
   - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
@@ -88,9 +93,9 @@
     - `kallisto_index`: Create a kallisto index (PR #149).
     - `kallisto_quant`: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads (PR #152).
 
-
 * `trimgalore`: Quality and adapter trimming for fastq files (PR #117). 
 
+
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1` (PR #72).

diff --git a/src/agat/agat_sp_add_introns/config.vsh.yaml b/src/agat/agat_sp_add_introns/config.vsh.yaml
@@ -0,0 +1,64 @@
+name: agat_sp_add_introns
+namespace: agat
+description: |
+  Add intronic elements to a gtf/gff file without intron features.
+keywords: [gene annotations, GTF conversion]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_add_introns.html
+  issue_tracker: https://github.com/NBISweden/AGAT/issues
+  repository: https://github.com/NBISweden/AGAT
+references: 
+  doi: 10.5281/zenodo.3552717
+license: GPL-3.0
+requirements:
+  commands: [agat]
+authors:
+  - __merge__: /src/_authors/leila_paquay.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --gff
+        alternatives: [-f, --ref, --reffile]
+        description: Input GTF/GFF file.
+        type: file
+        required: true
+        example: input.gff
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile, --gtf]
+        description: Output GFF3 file.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --config
+        alternatives: [-c]
+        description: |
+          AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option 
+          gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+        type: file
+        example: custom_agat_config.yaml
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
diff --git a/src/agat/agat_sp_add_introns/help.txt b/src/agat/agat_sp_add_introns/help.txt
@@ -0,0 +1,62 @@
+```sh
+agat_sp_add_introns.pl --help
+```
+
+  ------------------------------------------------------------------------------
+|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
+|   https://github.com/NBISweden/AGAT                                          |
+|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
+ ------------------------------------------------------------------------------
+
+
+Name:
+    agat_sp_add_introns.pl
+
+Description:
+    The script aims to add intron features to gtf/gff file without intron
+    features.
+
+Usage:
+        agat_sp_add_introns.pl --gff infile --out outFile
+        agat_sp_add_introns.pl --help
+
+Options:
+    --gff, -f, --ref or -reffile
+            Input GTF/GFF file.
+
+    --out, --output or -o
+            Output GFF3 file.
+
+    -c or --config
+            String - Input agat config file. By default AGAT takes as input
+            agat_config.yaml file from the working directory if any,
+            otherwise it takes the orignal agat_config.yaml shipped with
+            AGAT. To get the agat_config.yaml locally type: "agat config
+            --expose". The --config option gives you the possibility to use
+            your own AGAT config file (located elsewhere or named
+            differently).
+
+    --help or -h
+            Display this helpful text.
+
+Feedback:
+  Did you find a bug?:
+    Do not hesitate to report bugs to help us keep track of the bugs and
+    their resolution. Please use the GitHub issue tracking system available
+    at this address:
+
+                https://github.com/NBISweden/AGAT/issues
+
+     Ensure that the bug was not already reported by searching under Issues.
+     If you're unable to find an (open) issue addressing the problem, open a new one.
+     Try as much as possible to include in the issue when relevant:
+     - a clear description,
+     - as much relevant information as possible,
+     - the command used,
+     - a data sample,
+     - an explanation of the expected behaviour that is not occurring.
+
+  Do you want to contribute?:
+    You are very welcome, visit this address for the Contributing
+    guidelines:
+    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
diff --git a/src/agat/agat_sp_add_introns/script.sh b/src/agat/agat_sp_add_introns/script.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+agat_sp_add_introns.pl \
+  -f "$par_gff" \
+  -o "$par_output" \
+  ${par_config:+--config "${par_config}"}
diff --git a/src/agat/agat_sp_add_introns/test.sh b/src/agat/agat_sp_add_introns/test.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+
+# create temporary directory and clean up on exit
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --gff "$test_dir/1_truncated.gff" \
+  --output "$TMPDIR/output.gff" 
+
+echo ">> Checking output"
+[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$TMPDIR/output.gff" "$test_dir/test_output.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+echo "> Test successful"
diff --git a/src/agat/agat_sp_add_introns/test_data/1_truncated.gff b/src/agat/agat_sp_add_introns/test_data/1_truncated.gff
@@ -0,0 +1,106 @@
+##gff-version 3
+##sequence-region   1 1 43270923
+#!genome-build RAP-DB IRGSP-1.0
+#!genome-version IRGSP-1.0
+#!genome-date 2015-10
+#!genome-build-accession GCA_001433935.1
+1	RAP-DB	chromosome	1	43270923	.	.	.	ID=chromosome:1;Alias=Chr1,AP014957.1,NC_029256.1
+###
+1	irgsp	repeat_region	2000	2100	.	+	.	ID=fakeRepeat1
+###
+1	irgsp	gene	2983	10815	.	+	.	ID=gene:Os01g0100100;biotype=protein_coding;description=RabGAP/TBC domain containing protein. (Os01t0100100-01);gene_id=Os01g0100100;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	2983	10815	.	+	.	ID=transcript:Os01t0100100-01;Parent=gene:Os01g0100100;biotype=protein_coding;transcript_id=Os01t0100100-01
+1	irgsp	exon	2983	3268	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon1;rank=1
+1	irgsp	five_prime_UTR	2983	3268	.	+	.	Parent=transcript:Os01t0100100-01
+1	irgsp	five_prime_UTR	3354	3448	.	+	.	Parent=transcript:Os01t0100100-01
+1	irgsp	exon	3354	3616	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100100-01.exon2;rank=2
+1	irgsp	CDS	3449	3616	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	4357	4455	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon3;rank=3
+1	irgsp	CDS	4357	4455	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	5457	5560	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100100-01.exon4;rank=4
+1	irgsp	CDS	5457	5560	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	7136	7944	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon5;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100100-01.exon5;rank=5
+1	irgsp	CDS	7136	7944	.	+	1	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	8028	8150	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=Os01t0100100-01.exon6;rank=6
+1	irgsp	CDS	8028	8150	.	+	2	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	8232	8320	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon7;rank=7
+1	irgsp	CDS	8232	8320	.	+	2	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	8408	8608	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100100-01.exon8;rank=8
+1	irgsp	CDS	8408	8608	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	9210	9615	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon9;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100100-01.exon9;rank=9
+1	irgsp	CDS	9210	9615	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	10102	10187	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon10;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100100-01.exon10;rank=10
+1	irgsp	CDS	10102	10187	.	+	2	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	CDS	10274	10297	.	+	0	ID=CDS:Os01t0100100-01;Parent=transcript:Os01t0100100-01;protein_id=Os01t0100100-01
+1	irgsp	exon	10274	10430	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon11;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100100-01.exon11;rank=11
+1	irgsp	three_prime_UTR	10298	10430	.	+	.	Parent=transcript:Os01t0100100-01
+1	irgsp	exon	10504	10815	.	+	.	Parent=transcript:Os01t0100100-01;Name=Os01t0100100-01.exon12;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100100-01.exon12;rank=12
+1	irgsp	three_prime_UTR	10504	10815	.	+	.	Parent=transcript:Os01t0100100-01
+###
+1	irgsp	gene	11218	12435	.	+	.	ID=gene:Os01g0100200;biotype=protein_coding;description=Conserved hypothetical protein. (Os01t0100200-01);gene_id=Os01g0100200;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	11218	12435	.	+	.	ID=transcript:Os01t0100200-01;Parent=gene:Os01g0100200;biotype=protein_coding;transcript_id=Os01t0100200-01
+1	irgsp	five_prime_UTR	11218	11797	.	+	.	Parent=transcript:Os01t0100200-01
+1	irgsp	exon	11218	12060	.	+	.	Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100200-01.exon1;rank=1
+1	irgsp	CDS	11798	12060	.	+	0	ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
+1	irgsp	CDS	12152	12317	.	+	1	ID=CDS:Os01t0100200-01;Parent=transcript:Os01t0100200-01;protein_id=Os01t0100200-01
+1	irgsp	exon	12152	12435	.	+	.	Parent=transcript:Os01t0100200-01;Name=Os01t0100200-01.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100200-01.exon2;rank=2
+1	irgsp	three_prime_UTR	12318	12435	.	+	.	Parent=transcript:Os01t0100200-01
+###
+1	irgsp	gene	11372	12284	.	-	.	ID=gene:Os01g0100300;biotype=protein_coding;description=Cytochrome P450 domain containing protein. (Os01t0100300-00);gene_id=Os01g0100300;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	11372	12284	.	-	.	ID=transcript:Os01t0100300-00;Parent=gene:Os01g0100300;biotype=protein_coding;transcript_id=Os01t0100300-00
+1	irgsp	exon	11372	12042	.	-	.	Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100300-00.exon2;rank=2
+1	irgsp	CDS	11372	12042	.	-	2	ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
+1	irgsp	exon	12146	12284	.	-	.	Parent=transcript:Os01t0100300-00;Name=Os01t0100300-00.exon1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=Os01t0100300-00.exon1;rank=1
+1	irgsp	CDS	12146	12284	.	-	0	ID=CDS:Os01t0100300-00;Parent=transcript:Os01t0100300-00;protein_id=Os01t0100300-00
+###
+1	irgsp	gene	12721	15685	.	+	.	ID=gene:Os01g0100400;biotype=protein_coding;description=Similar to Pectinesterase-like protein. (Os01t0100400-01);gene_id=Os01g0100400;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	12721	15685	.	+	.	ID=transcript:Os01t0100400-01;Parent=gene:Os01g0100400;biotype=protein_coding;transcript_id=Os01t0100400-01
+1	irgsp	five_prime_UTR	12721	12773	.	+	.	Parent=transcript:Os01t0100400-01
+1	irgsp	exon	12721	13813	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100400-01.exon1;rank=1
+1	irgsp	CDS	12774	13813	.	+	0	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	exon	13906	14271	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100400-01.exon2;rank=2
+1	irgsp	CDS	13906	14271	.	+	1	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	exon	14359	14437	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=Os01t0100400-01.exon3;rank=3
+1	irgsp	CDS	14359	14437	.	+	1	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	exon	14969	15171	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100400-01.exon4;rank=4
+1	irgsp	CDS	14969	15171	.	+	0	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	CDS	15266	15359	.	+	1	ID=CDS:Os01t0100400-01;Parent=transcript:Os01t0100400-01;protein_id=Os01t0100400-01
+1	irgsp	exon	15266	15685	.	+	.	Parent=transcript:Os01t0100400-01;Name=Os01t0100400-01.exon5;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=Os01t0100400-01.exon5;rank=5
+1	irgsp	three_prime_UTR	15360	15685	.	+	.	Parent=transcript:Os01t0100400-01
+###
+1	irgsp	gene	12808	13978	.	-	.	ID=gene:Os01g0100466;biotype=protein_coding;description=Hypothetical protein. (Os01t0100466-00);gene_id=Os01g0100466;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	12808	13978	.	-	.	ID=transcript:Os01t0100466-00;Parent=gene:Os01g0100466;biotype=protein_coding;transcript_id=Os01t0100466-00
+1	irgsp	three_prime_UTR	12808	12868	.	-	.	Parent=transcript:Os01t0100466-00
+1	irgsp	exon	12808	13782	.	-	.	Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon2;rank=2
+1	irgsp	CDS	12869	13102	.	-	0	ID=CDS:Os01t0100466-00;Parent=transcript:Os01t0100466-00;protein_id=Os01t0100466-00
+1	irgsp	five_prime_UTR	13103	13782	.	-	.	Parent=transcript:Os01t0100466-00
+1	irgsp	exon	13880	13978	.	-	.	Parent=transcript:Os01t0100466-00;Name=Os01t0100466-00.exon1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100466-00.exon1;rank=1
+1	irgsp	five_prime_UTR	13880	13978	.	-	.	Parent=transcript:Os01t0100466-00
+###
+1	irgsp	gene	16399	20144	.	+	.	ID=gene:Os01g0100500;biotype=protein_coding;description=Immunoglobulin-like domain containing protein. (Os01t0100500-01);gene_id=Os01g0100500;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	16399	20144	.	+	.	ID=transcript:Os01t0100500-01;Parent=gene:Os01g0100500;biotype=protein_coding;transcript_id=Os01t0100500-01
+1	irgsp	five_prime_UTR	16399	16598	.	+	.	Parent=transcript:Os01t0100500-01
+1	irgsp	exon	16399	16976	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=Os01t0100500-01.exon1;rank=1
+1	irgsp	CDS	16599	16976	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	17383	17474	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=Os01t0100500-01.exon2;rank=2
+1	irgsp	CDS	17383	17474	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	17558	18258	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=Os01t0100500-01.exon3;rank=3
+1	irgsp	CDS	17558	18258	.	+	1	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	18501	18571	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=Os01t0100500-01.exon4;rank=4
+1	irgsp	CDS	18501	18571	.	+	2	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	18968	19057	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon5;rank=5
+1	irgsp	CDS	18968	19057	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	19142	19321	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=Os01t0100500-01.exon6;rank=6
+1	irgsp	CDS	19142	19321	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	CDS	19531	19593	.	+	0	ID=CDS:Os01t0100500-01;Parent=transcript:Os01t0100500-01;protein_id=Os01t0100500-01
+1	irgsp	exon	19531	19629	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon7;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=Os01t0100500-01.exon7;rank=7
+1	irgsp	three_prime_UTR	19594	19629	.	+	.	Parent=transcript:Os01t0100500-01
+1	irgsp	exon	19734	20144	.	+	.	Parent=transcript:Os01t0100500-01;Name=Os01t0100500-01.exon8;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=Os01t0100500-01.exon8;rank=8
+1	irgsp	three_prime_UTR	19734	20144	.	+	.	Parent=transcript:Os01t0100500-01
+###
+1	irgsp	gene	22841	26892	.	+	.	ID=gene:Os01g0100600;biotype=protein_coding;description=Single-stranded nucleic acid binding R3H domain containing protein. (Os01t0100600-01);gene_id=Os01g0100600;logic_name=irgspv1.0-20170804-genes
+1	irgsp	mRNA	22841	26892	.	+	.	ID=transcript:Os01t0100600-01;Parent=gene:Os01g0100600;biotype=protein_coding;transcript_id=Os01t0100600-01
+1	irgsp	five_prime_UTR	22841	23231	.	+	.	Parent=transcript:Os01t0100600-01
+1	irgsp	exon	22841	23281	.	+	.	Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=Os01t0100600-01.exon1;rank=1
+1	irgsp	CDS	23232	23281	.	+	0	ID=CDS:Os01t0100600-01;Parent=transcript:Os01t0100600-01;protein_id=Os01t0100600-01
+1	irgsp	exon	23572	23847	.	+	.	Parent=transcript:Os01t0100600-01;Name=Os01t0100600-01.exon2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=Os01t0100600-01.exon2;rank=2
diff --git a/src/agat/agat_sp_add_introns/test_data/script.sh b/src/agat/agat_sp_add_introns/test_data/script.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+# clone repo
+if [ ! -d /tmp/agat_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
+fi
+
+# copy test data
+cp -r /tmp/agat_source/t/scripts_output/in/1.gff src/agat/agat_sp_add_introns/test_data
+cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_add_introns_1.gff src/agat/agat_sp_add_introns/test_data
+
+head -n 106 "src/agat/agat_sp_add_introns/test_data/1.gff" > "src/agat/agat_sp_add_introns/test_data/1_truncated.gff"