Add agat sp compare two annotations

CHANGELOG.md

@@ -23,6 +23,7 @@
   - `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
   - `agat/agat_convert_bed2gff`: convert bed file to gff format (PR #97).
   - `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
+  - `agat/agat_sp_compare_two_annotations`: compare two annotation of the same assembly (PR #127).
   - `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).
 

src/agat/agat_sp_compare_two_annotations/config.vsh.yaml

@@ -0,0 +1,97 @@
+name: agat_sp_compare_two_annotations
+namespace: agat
+description: |
+  The script aims to compare two annotation of the same assembly. It
+  provides information about split/fusion of genes between the two
+  annotations. The most common cases are: 
+
+    * 1 => 0 ( gene uniq to file1) 
+    * 0 => 1 ( gene uniq to file2) 
+    * 1 => 1 ( 1 gene from file 1 overlaps only 1 gene from file2) 
+    * 1 => <many> ( 1 gene from file 1 overlaps <many> genes
+  from file2)
+    * => split case (with file 1 as reference) 
+    * <many> => 1 (<many> genes from file 1 overlap only 1 gene from file2)
+    * => fusion case (with file 1 as reference)
+
+  Then you can get more complex cases: 
+
+    * <many> => <many> (<many> genes from file 1 overlap <many> genes from file2)
+
+  The script output a folder containing a report of number of different
+  cases as well as a file per case type listing per line the gene
+  feature's ID involved in each case.
+keywords: [gene annotations, GFF]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_compare_two_annotations.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: --gff1
+        description: Input GTF/GFF file1.
+        type: file
+        required: true
+        direction: input
+        example: input1.gff
+      - name: --gff2
+        description: Input GTF/GFF file2.
+        type: file
+        required: true
+        direction: input
+        example: input2.gff
+  - name: Outputs
+    arguments:       
+      - name: --output_dir
+        alternatives: [-o, --out, --output]
+        description: |
+          Output folder. It contains a report that summarizes the type and number of cases, as well as a file per case type containing one case per line with the list of gene feature's ID (or other type of feature level1) from file1 then file2 separated by a |.
+        type: file
+        direction: output
+        required: true
+        example: output_folder
+  - name: Arguments
+    arguments:
+      - name: --debug
+        alternatives: [-d]
+        description: Debug option, makes it easier to follow what is going on for debugging purposes.
+        type: boolean_true
+      - name: --verbose
+        alternatives: [-v]
+        description: Verbose option, makes it easier to follow what is going on.
+        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_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_compare_two_annotations/help.txt

@@ -0,0 +1,86 @@
+```sh
+agat_sp_compare_two_annotations.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_compare_two_annotations.pl
+
+Description:
+    The script aims to compare two annotation of the same assembly. It
+    provided information about split/fusion of genes between the two
+    annotations. The most common cases are: 1 => 0 ( gene uniq to file1) 0
+    => 1 ( gene uniq to file2) 1 => 1 ( 1 gene from file 1 overlaps only 1
+    gene from file2) 1 => <many> ( 1 gene from file 1 overlaps <many> genes
+    from file2) => split case (with file 1 as reference) <many> => 1 (
+    <many> genes from file 1 overlap only 1 gene from file2) => fusion case
+    (with file 1 as reference)
+
+    Then you can get more complex cases: <many> => <many> (<many> genes from
+    file 1 overlap <many> genes from file2)
+
+    The script output a folder containing a report of number of different
+    cases as well as a file per case type listing per line the gene
+    feature's ID involved in each case.
+
+Usage:
+        agat_sp_compare_two_annotations.pl -gff1 infile.gff [ -o outfile ]
+        agat_sp_compare_two_annotations.pl --help
+
+Options:
+    -gff1   Input GTF/GFF file1.
+
+    -gff2   Input GTF/GFF file2.
+
+    -o , --output or --out
+            Output folder. It contains a report that resume the type and
+            number of cases, as well as a file per case type containing one
+            case per line with the list of gene feature's ID (or other type
+            of feature level1) from file1 then file2 separated by a |.
+
+    --debug or -d
+            Debug option, make it easier to follow what is going on for
+            debugging purpose.
+
+    --verbose or -v
+            Verbose option, make it easier to follow what is going on.
+
+    -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_sp_compare_two_annotations/script.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_debug" == "false" ]] && unset par_debug
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+# Debug statement to check if par_output_dir is set
+echo "par_output_dir is set to: ${par_output_dir}"
+
+# Ensure par_output_dir is set
+if [ -z "$par_output_dir" ]; then
+  echo "Error: par_output_dir is not set."
+  exit 1
+fi
+
+# run agat_sp_compare_two_annotations.pl
+agat_sp_compare_two_annotations.pl \
+  -gff1 "$par_gff1" \
+  -gff2 "$par_gff2" \
+  ${par_output_dir:+-o "${par_output_dir}"} \
+  ${par_debug:+--debug} \
+  ${par_verbose:+--verbose} \
+  ${par_config:+--config "${par_config}"}

src/agat/agat_sp_compare_two_annotations/test.sh

@@ -0,0 +1,78 @@
+#!/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 $meta_name with test data: identical files"
+"$meta_executable" \
+  --gff1 "$test_dir/1.gff" \
+  --gff2 "$test_dir/1.gff" \
+  --output_dir "$TMPDIR/output"
+
+echo ">> Checking output"
+[ ! -f "$TMPDIR/output/report.txt" ] && echo "Output file report.txt does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$TMPDIR/output/report.txt" ] && echo "Output file report.txt is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff <(tail -n +2 "$TMPDIR/output/report.txt") <(tail -n +2 "$test_dir/agat_sp_compare_two_annotations_1.txt")
+if [ $? -ne 0 ]; then
+  echo "Output file report.txt does not match expected output"
+  exit 1
+fi
+
+rm -rf $TMPDIR/output
+
+echo "> Run $meta_name with test data: different files"
+"$meta_executable" \
+  --gff1 "$test_dir/file1.gff" \
+  --gff2 "$test_dir/file2.gff" \
+  --output_dir "$TMPDIR/output"
+
+echo ">> Checking output"
+[ ! -f "$TMPDIR/output/report.txt" ] && echo "Output file report.txt does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$TMPDIR/output/report.txt" ] && echo "Output file report.txt is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff <(tail -n +2 "$TMPDIR/output/report.txt") <(tail -n +2 "$test_dir/agat_sp_compare_two_annotations_2.txt")
+if [ $? -ne 0 ]; then
+  echo "Output file report.txt does not match expected output"
+  exit 1
+fi
+
+rm -rf $TMPDIR/output
+
+echo "> Run $meta_name with test data: different files"
+"$meta_executable" \
+  --gff1 "$test_dir/file2.gff" \
+  --gff2 "$test_dir/file1.gff" \
+  --output_dir "$TMPDIR/output"
+
+echo ">> Checking output"
+[ ! -f "$TMPDIR/output/report.txt" ] && echo "Output file report.txt does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$TMPDIR/output/report.txt" ] && echo "Output file report.txt is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff <(tail -n +2 "$TMPDIR/output/report.txt") <(tail -n +2 "$test_dir/agat_sp_compare_two_annotations_3.txt")
+if [ $? -ne 0 ]; then
+  echo "Output file report.txt does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"