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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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#!/bin/bash | ||
|
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set -eo pipefail | ||
|
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## 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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#!/bin/bash | ||
|
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set -eo pipefail | ||
|
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## VIASH START | ||
## VIASH END | ||
|
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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" | ||
|
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echo ">> Checking output" | ||
[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1 | ||
|
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echo ">> Check if output is empty" | ||
[ ! -s "$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" |
Oops, something went wrong.