Add agat sp add start and stop

CHANGELOG.md

@@ -25,6 +25,7 @@
   - `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
   - `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).
+  - `agat/agat_sp_add_start_and_stop`: adds start and stop codons when a CDS feature exists (PR #122).
 
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).

src/agat/agat_sp_add_start_and_stop/config.vsh.yaml

@@ -0,0 +1,92 @@
+name: agat_sp_add_start_and_stop
+namespace: agat
+description: |
+  The script adds start and stop codons when a CDS feature exists. The
+  script looks at the nucleotide sequence and checks the presence of start
+  and stop codons. The script works even if the start or stop codon are
+  split over several CDS features.
+keywords: [gene annotations, CDS, GFF]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_add_start_and_stop.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: [-i, -g]
+        description: Input GTF/GFF file.
+        type: file
+        required: true
+        direction: input
+        example: input.gff
+      - name: --fasta
+        alternatives: [--fa, -f]
+        description: Input fasta file. Needed to check that CDS sequences start by start codon and stop by stop codon.
+        type: file
+        required: true
+        direction: input
+        example: input.fasta
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: [--out, -o]
+        description: Output gff file updated.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --codon
+        alternatives: [--ct, --table]
+        description: Codon table to use. [default 1]
+        type: integer
+        required: false
+        example: 1
+      - name: --extend
+        alternatives: [-e]
+        description: When no start/stop codon found, try to extend the CDS to meet the next start/stop codon in the sequence.
+        type: boolean_true
+      - name: --ni
+        alternatives: [--na]
+        description: no iupac / no ambiguous, avoid usage of IUPAC. By default IUPAC is used that means, NNN is seen as start and/or stop codon.
+        type: boolean_true
+      - name: --verbose
+        alternatives: [-v]
+        description: Verbose for debugging purpose.
+        type: boolean_true
+      - 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
+        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_sp_add_start_and_stop/help.txt

@@ -0,0 +1,82 @@
+```sh
+agat_sp_add_start_and_stop.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_start_and_stop.pl.pl
+
+Description:
+    The script adds start and stop codons when a CDS feature exists. The
+    script looks at the nucleotide sequence and checks the presence of start
+    and stop codons. The script works even if the start or stop codon are
+    split over several CDS features.
+
+Usage:
+        agat_sp_add_start_and_stop.pl.pl --gff infile.gff --fasta genome.fa --out outfile.gff
+        agat_sp_add_start_and_stop.pl.pl --help
+
+Options:
+    --gff, -i or -g
+            Input GTF/GFF file.
+
+    --fasta, --fa or -f
+            Input fasta file. Needed to check that CDS sequences start by
+            start codon and stop by stop codon.
+
+    --ct, --codon or --table
+            Codon table to use. [default 1]
+
+    --out, --output or -o
+            Output gff file updated
+
+    -e or --extend
+            Boolean - When no start/stop codon found, try to extend the CDS
+            to meet the next start/stop codon in the sequence.
+
+    --ni or --na
+            Boolean - no iupac / no ambiguous, avoid usage of IUPAC. By
+            default IUPAC is used that means, NNN is seen as start and/or
+            stop codon.
+
+    -v      Verbose for debugging purpose.
+
+    -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

src/agat/agat_sp_add_start_and_stop/script.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_ni" == "false" ]] && unset par_ni
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+[[ "$par_extend" == "false" ]] && unset par_extend
+
+# run agat_sp_add_start_and_stop.pl
+agat_sp_add_start_and_stop.pl \
+  --gff "$par_gff" \
+  --fasta "$par_fasta" \
+  --output "$par_output" \
+  ${par_ct:+--ct "${par_ct}"} \
+  ${par_extend:+--extend} \
+  ${par_ni:+--ni} \
+  ${par_verbose:+--v} \
+  ${par_config:+--config "${par_config}"}

src/agat/agat_sp_add_start_and_stop/test.sh

@@ -0,0 +1,63 @@
+#!/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 $meta_name with test data and ni flag"
+"$meta_executable" \
+  --gff "$test_dir/agat_sp_add_start_and_stop.gff" \
+  --fasta "$test_dir/1.fa" \
+  --output "$TMPDIR/output.gff" \
+  --ni 
+
+echo ">> Checking output"
+[ ! -f "$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/agat_sp_add_start_and_stop_1.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+rm -f "$TMPDIR/output.gff"
+
+echo "> Run $meta_name with test data and ni flag"
+"$meta_executable" \
+  --gff "$test_dir/agat_sp_add_start_and_stop.gff" \
+  --fasta "$test_dir/1.fa" \
+  --output "$TMPDIR/output.gff" \
+  --ni \
+  --extend
+
+
+echo ">> Checking output"
+[ ! -f "$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/agat_sp_add_start_and_stop_2.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+rm -f "$TMPDIR/output.gff"
+
+echo "> Test successful"