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 +1,89 @@
+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. Required 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.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --codon
+        alternatives: [--ct, --table]
+        description: Codon table to use. By default, codon table 1 is used, allowing for start codons TTG, CTG and ATG. Codon table 0 strictly uses ATG only as start codon. For further available codon tables, see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1.
+        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: Avoid usage of IUPAC. By default IUPAC is used, meaning NNN is seen as start and/or stop codon.
+        type: boolean_true
+      - name: --verbose
+        alternatives: [-v]
+        description: Add verbosity.
+        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"