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| name: agat_convert_genscan2gff | ||
| namespace: agat | ||
| description: | | ||
| The script takes a GENSCAN file as input, and will translate it in gff | ||
| format. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html). | ||
| **Known problem** | ||
| You must have submited only DNA sequence, without any header!! Indeed the tool expects only DNA | ||
| sequences and does not crash/warn if an header is submited along the | ||
| sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first | ||
| nucleotides of the sequence. Then all prediction location are shifted | ||
| accordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html). | ||
| I don't know if there is the same problem elsewhere.) | ||
| keywords: [gene annotations, GFF conversion, GENSCAN] | ||
| links: | ||
| homepage: https://github.com/NBISweden/AGAT | ||
| documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_genscan2gff.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: --genscan | ||
| alternatives: [-g] | ||
| description: Input genscan bed file that will be converted. | ||
| type: file | ||
| required: true | ||
| direction: input | ||
| - name: Outputs | ||
| arguments: | ||
| - name: --output | ||
| alternatives: [-o, --out, --outfile, --gff] | ||
| description: Output GFF file. If no output file is specified, the output will be written to STDOUT. | ||
| type: file | ||
| direction: output | ||
| required: true | ||
| example: output.gff | ||
| - name: Arguments | ||
| arguments: | ||
| - name: --source | ||
| description: | | ||
| The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data] | ||
| type: string | ||
| required: false | ||
| example: Stringtie | ||
| - name: --primary_tag | ||
| description: | | ||
| The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene] | ||
| type: string | ||
| required: false | ||
| example: gene | ||
| - name: --inflate_type | ||
| description: | | ||
| Feature type (3rd column in gff) created when inflate parameter activated [default: exon]. | ||
| type: string | ||
| required: false | ||
| example: exon | ||
| - name: --verbose | ||
| 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 |
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| ```sh | ||
| agat_convert_genscan2gff.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_genscan2gff.pl | ||
|
|
||
| Description: | ||
| The script takes a genscan file as input, and will translate it in gff | ||
| format. The genscan format is described here: | ||
| http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/gens | ||
| can.html /!\ vvv Known problem vvv /!\ You must have submited only DNA | ||
| sequence, wihtout any header!! Indeed the tool expects only DNA | ||
| sequences and does not crash/warn if an header is submited along the | ||
| sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first | ||
| nucleotides of the sequence. Then all prediction location are shifted | ||
| accordingly. (checked only on the online version | ||
| http://argonaute.mit.edu/GENSCAN.html. I don't know if there is the same | ||
| pronlem elsewhere.) /!\ ^^^ Known problem ^^^^ /!\ | ||
|
|
||
| Usage: | ||
| agat_convert_genscan2gff.pl --genscan infile.bed [ -o outfile ] | ||
| agat_convert_genscan2gff.pl -h | ||
|
|
||
| Options: | ||
| --genscan or -g | ||
| Input genscan bed file that will be convert. | ||
|
|
||
| --source | ||
| The source informs about the tool used to produce the data and | ||
| is stored in 2nd field of a gff file. Example: | ||
| Stringtie,Maker,Augustus,etc. [default: data] | ||
|
|
||
| --primary_tag | ||
| The primary_tag corresponf to the data type and is stored in 3rd | ||
| field of a gff file. Example: gene,mRNA,CDS,etc. [default: gene] | ||
|
|
||
| --inflate_off | ||
| By default we inflate the block fields (blockCount, blockSizes, | ||
| blockStarts) to create subfeatures of the main feature | ||
| (primary_tag). Type of subfeature created based on the | ||
| inflate_type parameter. If you don't want this inflating | ||
| behaviour you can deactivate it by using the option | ||
| --inflate_off. | ||
|
|
||
| --inflate_type | ||
| Feature type (3rd column in gff) created when inflate parameter | ||
| activated [default: exon]. | ||
|
|
||
| --verbose | ||
| add verbosity | ||
|
|
||
| -o , --output , --out , --outfile or --gff | ||
| 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| #!/bin/bash | ||
|
|
||
| set -eo pipefail | ||
|
|
||
| ## VIASH START | ||
| ## VIASH END | ||
|
|
||
| # unset flags | ||
| [[ "$par_inflate_off" == "true" ]] && unset par_inflate_off | ||
| [[ "$par_verbose" == "false" ]] && unset par_verbose | ||
|
|
||
| # run agat_convert_genscan2gff | ||
| agat_convert_genscan2gff.pl \ | ||
| --genscan "$par_genscan" \ | ||
| --output "$par_output" \ | ||
| ${par_source:+--source "${par_source}"} \ | ||
| ${par_primary_tag:+--primary_tag "${par_primary_tag}"} \ | ||
| ${par_inflate_off:+--inflate_off} \ | ||
| ${par_inflate_type:+--inflate_type "${par_inflate_type}"} \ | ||
| ${par_verbose:+--verbose} \ | ||
| ${par_config:+--config "${par_config}"} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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_name-XXXXXX") | ||
| function clean_up { | ||
| [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR" | ||
| } | ||
| trap clean_up EXIT | ||
|
|
||
| echo "> Run $meta_name with test data" | ||
| "$meta_executable" \ | ||
| --genscan "$test_dir/test.genscan" \ | ||
| --output "$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_genscan2gff_1.gff" | ||
| if [ $? -ne 0 ]; then | ||
| echo "Output file output.gff does not match expected output" | ||
| exit 1 | ||
| fi | ||
|
|
||
| echo "> Test successful" |
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src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| ##gff-version 3 | ||
| unknown genscan gene 2223 4605 75.25 + . ID=gene_1 | ||
| unknown genscan mRNA 2223 4605 75.25 + . ID=mrna_1;Parent=gene_1 | ||
| unknown genscan exon 2223 3020 75.25 + . ID=exon_1;Parent=mrna_1 | ||
| unknown genscan exon 4249 4605 13.03 + . ID=exon_2;Parent=mrna_1 | ||
| unknown genscan CDS 2223 3020 75.25 + 0 ID=cds_1;Parent=mrna_1 | ||
| unknown genscan CDS 4249 4605 13.03 + 0 ID=cds_2;Parent=mrna_1 | ||
| unknown genscan gene 6829 8789 20.06 - . ID=gene_2 | ||
| unknown genscan mRNA 6829 8789 20.06 - . ID=mrna_2;Parent=gene_2 | ||
| unknown genscan exon 6829 7297 20.06 - . ID=exon_3;Parent=mrna_2 | ||
| unknown genscan exon 7730 7888 12.78 - . ID=exon_4;Parent=mrna_2 | ||
| unknown genscan exon 8029 8185 7.45 - . ID=exon_5;Parent=mrna_2 | ||
| unknown genscan exon 8278 8546 17.45 - . ID=exon_6;Parent=mrna_2 | ||
| unknown genscan exon 8647 8789 18.65 - . ID=exon_7;Parent=mrna_2 | ||
| unknown genscan CDS 6829 7297 20.06 - 1 ID=cds_3;Parent=mrna_2 | ||
| unknown genscan CDS 7730 7888 12.78 - 1 ID=cds_4;Parent=mrna_2 | ||
| unknown genscan CDS 8029 8185 7.45 - 2 ID=cds_5;Parent=mrna_2 | ||
| unknown genscan CDS 8278 8546 17.45 - 1 ID=cds_6;Parent=mrna_2 | ||
| unknown genscan CDS 8647 8789 18.65 - 0 ID=cds_7;Parent=mrna_2 | ||
| unknown genscan gene 10209 11924 16.18 + . ID=gene_3 | ||
| unknown genscan mRNA 10209 11924 16.18 + . ID=mrna_3;Parent=gene_3 | ||
| unknown genscan exon 10209 11313 16.18 + . ID=exon_8;Parent=mrna_3 | ||
| unknown genscan exon 11850 11924 3.27 + . ID=exon_9;Parent=mrna_3 | ||
| unknown genscan CDS 10209 11313 16.18 + 0 ID=cds_8;Parent=mrna_3 | ||
| unknown genscan CDS 11850 11924 3.27 + 2 ID=cds_9;Parent=mrna_3 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| #!/bin/bash | ||
|
|
||
| # clone repo | ||
| if [ ! -d /tmp/agat_source ]; then | ||
| git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source | ||
| fi | ||
|
|
||
| # copy test data | ||
| cp -r /tmp/agat_source/t/scripts_output/in/test.genscan src/agat/agat_convert_genscan2gff/test_data/test.genscan | ||
| cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_genscan2gff_1.gff src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff | ||
|
|
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