Add agat sp extract attributes

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_extract_attributes`: extract choosen attributes from a GFF file (PR #131).
 
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).

src/agat/agat_sp_extract_attributes/config.vsh.yaml

@@ -0,0 +1,113 @@
+name: agat_sp_extract_attributes
+namespace: agat
+description: |
+  The script takes a gtf/gff file as input. The script allows to extract
+  choosen attributes of all or specific feature types. The 9th column of a
+  gff/gtf file contains a list of attributes. An attribute (gff3) looks
+  like that `tag=value`.
+keywords: [gene annotations, GFF]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_extract_attributes.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]
+        description: Input GTF/GFF file.
+        type: file
+        required: true
+        direction: input
+        example: input.gff
+      - name: --attribute
+        alternatives: [--att, -a]
+        description: |
+          Attribute tag. The value of the attribute tag specified will be
+          extracted from the feature type specified by the option `-p`.
+        direction: input
+        multiple: true
+        type: string
+        required: true
+        example: protein_id
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile]
+        description: Output GFF file. One file per attribute tag will be created using the attribute tag name as file name suffix.
+        type: string
+        required: true
+        example: output.txt
+  - name: Arguments
+    arguments:
+      - name: --primary_tag
+        alternatives: [-p, -t, -l]
+        description: |
+          Primary tag option, case insensitive, list. Allow to specify the
+          feature types that will be handled. 
+
+          You can specify a specific feature by giving its primary tag name (column 3) as: 
+            * cds
+            * Gene
+            * mRNA
+
+          You can specify directly all the features of a particular
+          level: 
+
+            * level2=mRNA,ncRNA,tRNA,etc 
+            * level3=CDS,exon,UTR,etc. 
+
+          By default, all features are taken into account. Filling the option
+          with the value "all" will have the same behavior.
+        type: string
+        required: false
+        multiple: true
+        example: gene
+      - name: --merge
+        alternatives: [-m]
+        description: |
+          By default, the values of each attribute tag are written in its
+          dedicated file. To write the values of all tags in only one file,
+          use this option.
+        type: boolean_true
+      - name: --dot
+        alternatives: [-d]
+        description: |
+          By default, when an attribute is not found for a feature, a dot
+          (.) is reported. If you don't want anything to be printed in such
+          a case, use this option.
+        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_extract_attributes/help.txt

@@ -0,0 +1,88 @@
+```sh
+agat_sp_extract_attributes.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_extract_attributes.pl
+
+Description:
+    The script takes a gtf/gff file as input. The script allows to extract
+    choosen attributes of all or specific feature types. The 9th column of a
+    gff/gtf file contains a list of attributes. An attribute (gff3) looks
+    like that tag=value
+
+Usage:
+        agat_sp_extract_attributes.pl --gff file.gff  --att locus_tag,product,name -p level2,cds,exon [ -o outfile ]
+        agat_sp_extract_attributes.pl --help
+
+Options:
+    --gff or -f
+            Input GTF/GFF file.
+
+    -p, -t or -l
+            primary tag option, case insensitive, list. Allow to specied the
+            feature types that will be handled. You can specified a specific
+            feature by given its primary tag name (column 3) as: cds, Gene,
+            MrNa You can specify directly all the feature of a particular
+            level: level2=mRNA,ncRNA,tRNA,etc level3=CDS,exon,UTR,etc By
+            default all feature are taking in account. fill the option by
+            the value "all" will have the same behaviour.
+
+    --attribute, --att, -a
+            attribute tag. The value of the attribute tag specified will be
+            extracted from the feature type specified by the option -p. List
+            of attributes must be coma separated.
+
+    --merge or -m
+            By default the values of each attribute tag is writen in its
+            dedicated file. To write the values of all tags in only one file
+            use this option.
+
+    -d      By default when an attribute is not found for a feature, a dot
+            (.) is reported. If you don't want anything to be printed in
+            such case use this option.
+
+    -o , --output , --out or --outfile
+            Output GFF 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_sp_extract_attributes/script.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_merge" == "false" ]] && unset par_merge
+[[ "$par_dot" == "false" ]] && unset par_dot
+
+# run agat_sp_extract_attributes.pl
+agat_sp_extract_attributes.pl \
+  --gff "$par_gff" \
+  --attribute "$par_attribute" \
+  --output "$par_output" \
+  ${par_primary_tag:+-p "${par_primary_tag}"} \
+  ${par_merge:+--merge} \
+  ${par_dot:+-d} \
+  ${par_config:+--config "${par_config}"}

src/agat/agat_sp_extract_attributes/test.sh

@@ -0,0 +1,36 @@
+#!/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 "$test_dir/1.gff" \
+  --attribute protein_id \
+  --output "$TMPDIR/output.txt" 
+
+echo ">> Checking output"
+[ ! -f "$TMPDIR/output_protein_id.txt" ] && echo "Output file output_protein_id.txt does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$TMPDIR/output_protein_id.txt" ] && echo "Output file output_protein_id.txt is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$TMPDIR/output_protein_id.txt" "$test_dir/agat_sp_extract_attributes_1.txt"
+if [ $? -ne 0 ]; then
+  echo "Output file output_protein_id.txt does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"