Add agat convert sp gff2bed

CHANGELOG.md

@@ -20,8 +20,9 @@
                 based on a provided sequence IDs or region coordinates file (PR #85).
 
 * `agat`:
-  - `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_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
+  - `agat_convert_bed2gff`: convert bed file to gff format (PR #97).
+  - `agat_convert_sp_gff2bed`: convert GTF/GXF file into bed file (PR #114).
   - `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).

src/agat/agat_convert_sp_gff2bed/config.vsh.yaml

@@ -0,0 +1,105 @@
+name: agat_convert_sp_gff2bed
+namespace: agat
+description: |
+  The script aims to convert GTF/GXF file into bed file. It will convert
+  level2 features from gff (mRNA, transcripts) into bed features. If the
+  selected level2 subfeatures (defaut: exon) exist, they are reported in
+  the block fields (9-12th colum in bed). CDS Start and End are reported
+  in column 7 and 8 accordingly.
+
+  ### Definition of the bed format: 
+
+  #### Definition of the BED format:
+
+    1. **chrom** - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
+    2. **chromStart** - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
+    3. **chromEnd** - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
+
+  #### OPTIONAL fields:
+
+    4. **name** - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
+    5. **score** - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
+    6. **strand** - Defines the strand - either '+' or '-'.
+    7. **thickStart** - The starting position at which the feature is drawn thickly.
+    8. **thickEnd** - The ending position at which the feature is drawn thickly.
+    9. **itemRgb** - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RGB value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
+    10. **blockCount** - The number of blocks (exons) in the BED line.
+    11. **blockSizes** - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
+    12. **blockStarts** - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
+keywords: [gene annotations, GTF conversion, BED]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gff2bed.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]
+        description: Input GFF3 file that will be read.
+        type: file
+        required: true
+        direction: input
+        example: input.gff
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: [--outfile, --out, -o]
+        description: |
+          File where the result will be written.
+        type: file
+        direction: output
+        required: true
+        example: output.bed
+  - name: Arguments
+    arguments:
+      - name: --nc
+        description: |
+          Behaviour for non-coding features (e.g. records without CDS):
+
+            * keep: Default, they are kept but no CDS position is reported in the 7th and 8th columns (a period is reported instead).  
+            * filter: We remove them.  
+            * transcript: We keep them but values in the 7th and 8th columns will contain transcript's start and stop.  
+        type: string
+        choices: [keep, filter, transcript]
+        required: false
+      - name: --sub
+        description: |
+          Define the subfeature (level3, e.g. exon, cds, utr, etc.) to report as blocks in the BED output. Default: exon.
+        type: string
+        required: false
+        example: exon
+      - 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_convert_sp_gff2bed/help.txt

@@ -0,0 +1,105 @@
+```sh
+agat_convert_sp_gff2bed.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_gff2bed.pl
+
+Description:
+    The script aims to convert GTF/GXF file into bed file. It will convert
+    level2 features from gff (mRNA, transcripts) into bed features. If the
+    selected level2 subfeatures (defaut: exon) exist, they are reported in
+    the block fields (9-12th colum in bed). CDS Start and End are reported
+    in column 7 and 8 accordingly.
+
+    Definintion of the bed format: # 1 chrom - The name of the chromosome
+    (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671). # 2
+    chromStart - The starting position of the feature in the chromosome or
+    scaffold. The first base in a chromosome is numbered 0. # 3 chromEnd -
+    The ending position of the feature in the chromosome or scaffold. The
+    chromEnd base is not included in the display of the feature. For
+    example, the first 100 bases of a chromosome are defined as
+    chromStart=0, chromEnd=100, and span the bases numbered 0-99. ##########
+    OPTIONAL fields ########## # 4 name - Defines the name of the BED line.
+    This label is displayed to the left of the BED line in the Genome
+    Browser window when the track is open to full display mode or directly
+    to the left of the item in pack mode. # 5 score - A score between 0 and
+    1000. If the track line useScore attribute is set to 1 for this
+    annotation data set, the score value will determine the level of gray in
+    which this feature is displayed (higher numbers = darker gray). # 6
+    strand - Defines the strand - either '+' or '-'. # 7 thickStart - The
+    starting position at which the feature is drawn thickly # 8 thickEnd -
+    The ending position at which the feature is drawn thickly # 9 itemRgb -
+    An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb
+    attribute is set to "On", this RBG value will determine the display
+    color of the data contained in this BED line. NOTE: It is recommended
+    that a simple color scheme (eight colors or less) be used with this
+    attribute to avoid overwhelming the color resources of the Genome
+    Browser and your Internet browser. # 10 blockCount - The number of
+    blocks (exons) in the BED line. # 11 blockSizes - A comma-separated list
+    of the block sizes. The number of items in this list should correspond
+    to blockCount. # 12 blockStarts - A comma-separated list of block
+    starts. All of the blockStart positions should be calculated relative to
+    chromStart. The number of items in this list should correspond to
+    blockCount.
+
+Usage:
+        agat_convert_sp_gff2bed.pl --gff file.gff  [ -o outfile ]
+        agat_convert_sp_gff2bed.pl --help
+
+Options:
+    --gff   Input GFF3 file that will be read
+
+    --nc    STRING - behaviour for non-coding features (e.g. recored wihtout
+            CDS). [keep,filter,transcript] keep - Default, they are kept but
+            no CDS position is reported in the 7th and 8th columns (a period
+            is reported instead). filter - We remove them. transcript - We
+            keep them but values in 7th and 8th columns will contains
+            transcript's start and stop.
+
+    --sub   Define the subfeature (level3, e.g exon,cds,utr,etc...) to
+            report as blocks in the bed output. Defaut: exon.
+
+    --outfile, --out, --output, or -o
+            File where will be written the result. 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_gff2bed/script.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+agat_convert_sp_gff2bed.pl \
+  --gff "$par_gff" \
+  --output "$par_output" \
+  ${par_nc:+--nc "${par_nc}"} \
+  ${par_sub:+--sub "${par_sub}"} \
+  ${par_config:+--config "${par_config}"}

src/agat/agat_convert_sp_gff2bed/test.sh

@@ -0,0 +1,35 @@
+#!/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 "$test_dir/1.gff" \
+  --output "$TMPDIR/output.gff" 
+
+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_convert_sp_gff2bed_1.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"