Add agat convertspgff2gtf

CHANGELOG.md

@@ -73,6 +73,9 @@
     - `bedtools_getfasta`: extract sequences from a FASTA file for each of the
                            intervals defined in a BED/GFF/VCF file (PR #59).
 
+* `agat`:
+    - `agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
+
 ## MINOR CHANGES
 
 * Uniformize component metadata (PR #23).

src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml

@@ -0,0 +1,90 @@
+name: agat_convert_sp_gff2gtf
+namespace: agat
+description: |
+  The script aims to convert any GTF/GFF file into a proper GTF file. Full
+  information about the format can be found here:
+  https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7
+  different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the
+  version selected the script will filter out the features that are not
+  accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene
+  pseudogene) will be converted into gene feature and every level2 feature
+  (e.g mRNA ncRNA) will be converted into transcript feature. Using the
+  "relax" option you will produce a GTF-like output keeping all original
+  feature types (3rd column). No modification will occur e.g. mRNA to
+  transcript.
+
+  To be fully GTF compliant all feature have a gene_id and a transcript_id
+  attribute. The gene_id is unique identifier for the genomic source of
+  the transcript, which is used to group transcripts into genes. The
+  transcript_id is a unique identifier for the predicted transcript, which
+  is used to group features into transcripts.
+keywords: [gene annotations, GTF conversion]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/
+  issue_tracker: https://github.com/NBISweden/AGAT/issues
+  repository: https://github.com/NBISweden/AGAT
+references: 
+  doi: 10.5281/zenodo.3552717
+license: GPL-3.0
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --gff
+        alternatives: [-i]
+        description: Input GFF/GTF file that will be read
+        type: file
+        required: true
+        direction: input
+        example: input.gff
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile, --gtf]
+        description: Output GTF file. If no output file is specified, the output will be written to STDOUT.
+        type: file
+        direction: output
+        required: true
+        example: output.gtf
+  - name: Arguments
+    arguments:
+      - name: --gtf_version
+        description: |
+          Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax). Default value from AGAT config file (relax for the default config). The script option has the higher priority.  
+
+            * relax: all feature types are accepted.  
+            * GTF3 (9 feature types accepted): gene, transcript, exon, CDS, Selenocysteine, start_codon, stop_codon, three_prime_utr and five_prime_utr.  
+            * GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS, UTR, start_codon, stop_codon, Selenocysteine.  
+            * GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon.  
+            * GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon, exon, 5UTR, 3UTR.  
+            * GTF2 (4 feature types accepted): CDS, start_codon, stop_codon, exon.  
+            * GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon, intron.  
+        type: string
+        choices: [relax, "1", "2", "2.1", "2.2", "2.5", "3"]
+        required: false
+        example: "3"
+      - name: --config
+        alternatives: [-c]
+        description: |
+          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).
+        type: file
+        required: false
+        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

src/agat/agat_convert_sp_gff2gtf/help.txt

@@ -0,0 +1,102 @@
+```sh
+agat_convert_sp_gff2gtf.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_convert_sp_gff2gtf.pl
+
+Description:
+    The script aims to convert any GTF/GFF file into a proper GTF file. Full
+    information about the format can be found here:
+    https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7
+    different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the
+    version selected the script will filter out the features that are not
+    accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene
+    pseudogene) will be converted into gene feature and every level2 feature
+    (e.g mRNA ncRNA) will be converted into transcript feature. Using the
+    "relax" option you will produce a GTF-like output keeping all original
+    feature types (3rd column). No modification will occur e.g. mRNA to
+    transcript.
+
+    To be fully GTF compliant all feature have a gene_id and a transcript_id
+    attribute. The gene_id is unique identifier for the genomic source of
+    the transcript, which is used to group transcripts into genes. The
+    transcript_id is a unique identifier for the predicted transcript, which
+    is used to group features into transcripts.
+
+Usage:
+        agat_convert_sp_gff2gtf.pl --gff infile.gff [ -o outfile ]
+        agat_convert_sp_gff2gtf -h
+
+Options:
+    --gff, --gtf or -i
+            Input GFF/GTF file that will be read
+
+    --gtf_version version of the GTF output (1,2,2.1,2.2,2.5,3 or relax).
+    Default value from AGAT config file (relax for the default config). The
+    script option has the higher priority.
+            relax: all feature types are accepted.
+
+            GTF3 (9 feature types accepted): gene, transcript, exon, CDS,
+            Selenocysteine, start_codon, stop_codon, three_prime_utr and
+            five_prime_utr
+
+            GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS,
+            UTR, start_codon, stop_codon, Selenocysteine
+
+            GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon,
+            5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon
+
+            GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon,
+            exon, 5UTR, 3UTR
+
+            GTF2 (4 feature types accepted): CDS, start_codon, stop_codon,
+            exon
+
+            GTF1 (5 feature types accepted): CDS, start_codon, stop_codon,
+            exon, intron
+
+    -o , --output , --out , --outfile or --gtf
+            Output GTF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -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).
+
+    -h or --help
+            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
+

src/agat/agat_convert_sp_gff2gtf/script.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+agat_convert_sp_gff2gtf.pl \
+  -i "$par_gff" \
+  -o "$par_output" \
+  ${par_gtf_version:+--gtf_version "${par_gtf_version}"} \
+  ${par_config:+--config "${par_config}"}

src/agat/agat_convert_sp_gff2gtf/test.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --gff "$test_dir/0_test.gff" \
+  --output "output.gtf" 
+
+echo ">> Checking output"
+[ ! -f "output.gtf" ] && echo "Output file output.gtf does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "output.gtf" ] && echo "Output file output.gtf is empty" && exit 1
+
+echo ">> Check if the conversion resulted in the right GTF format"
+idGFF=$(head -n 2 "$test_dir/0_test.gff" | grep -o 'ID=[^;]*' | cut -d '=' -f 2-)
+expectedGTF="gene_id \"$idGFF\"; ID \"$idGFF\";"
+extractedGTF=$(head -n 3 "output.gtf" | grep -o 'gene_id "[^"]*"; ID "[^"]*";')
+[ "$extractedGTF" != "$expectedGTF" ] && echo "Output file output.gtf does not have the right format" && exit 1
+
+rm output.gtf
+
+echo "> Run $meta_name with test data and GTF version 2.5"
+"$meta_executable" \
+  --gff "$test_dir/0_test.gff" \
+  --output "output.gtf" \
+  --gtf_version "2.5"
+
+echo ">> Check if the output file header display the right GTF version"
+grep -q "##gtf-version 2.5" "output.gtf"
+[ $? -ne 0 ] && echo "Output file output.gtf header does not display the right GTF version" && exit 1
+
+echo "> Test successful"

src/agat/agat_convert_sp_gff2gtf/test_data/0_test.gff

@@ -0,0 +1,36 @@
+##gff-version 3
+scaffold625	maker	gene	337818	343277	.	+	.	ID=CLUHARG00000005458;Name=TUBB3_2
+scaffold625	maker	mRNA	337818	343277	.	+	.	ID=CLUHART00000008717;Parent=CLUHARG00000005458
+scaffold625	maker	exon	337818	337971	.	+	.	ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717
+scaffold625	maker	exon	340733	340841	.	+	.	ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717
+scaffold625	maker	exon	341518	341628	.	+	.	ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717
+scaffold625	maker	exon	341964	343277	.	+	.	ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717
+scaffold625	maker	CDS	337915	337971	.	+	0	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	CDS	340733	340841	.	+	0	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	CDS	341518	341628	.	+	2	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	CDS	341964	343033	.	+	2	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	five_prime_UTR	337818	337914	.	+	.	ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
+scaffold625	maker	three_prime_UTR	343034	343277	.	+	.	ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
+scaffold789	maker	gene	558184	564780	.	+	.	ID=CLUHARG00000003852;Name=PF11_0240
+scaffold789	maker	mRNA	558184	564780	.	+	.	ID=CLUHART00000006146;Parent=CLUHARG00000003852
+scaffold789	maker	exon	558184	560123	.	+	.	ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146
+scaffold789	maker	exon	561401	561519	.	+	.	ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146
+scaffold789	maker	exon	564171	564235	.	+	.	ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146
+scaffold789	maker	exon	564372	564780	.	+	.	ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146
+scaffold789	maker	CDS	558191	560123	.	+	0	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	CDS	561401	561519	.	+	2	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	CDS	564171	564235	.	+	0	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	CDS	564372	564588	.	+	1	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	five_prime_UTR	558184	558190	.	+	.	ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146
+scaffold789	maker	three_prime_UTR	564589	564780	.	+	.	ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146
+scaffold789	maker	mRNA	558184	564780	.	+	.	ID=CLUHART00000006147;Parent=CLUHARG00000003852
+scaffold789	maker	exon	558184	560123	.	+	.	ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147
+scaffold789	maker	exon	561401	561519	.	+	.	ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147
+scaffold789	maker	exon	562057	562121	.	+	.	ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147
+scaffold789	maker	exon	564372	564780	.	+	.	ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147
+scaffold789	maker	CDS	558191	560123	.	+	0	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	CDS	561401	561519	.	+	2	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	CDS	562057	562121	.	+	0	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	CDS	564372	564588	.	+	1	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	five_prime_UTR	558184	558190	.	+	.	ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147
+scaffold789	maker	three_prime_UTR	564589	564780	.	+	.	ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147

src/agat/agat_convert_sp_gff2gtf/test_data/script.sh

@@ -0,0 +1,9 @@
+#!/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/gff_syntax/in/0_test.gff src/agat/agat_convert_sp_gff2gtf/test_data