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GENIALbiologists-0.9.0
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مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
GENIAL: GENes Indentification with Abricate for Lucky biologists
| ویژگی | مقدار |
|---|---|
| سیستم عامل | POSIX :: Linux |
| نام فایل | GENIALbiologists-0.9.0 |
| نام | GENIALbiologists |
| نسخه کتابخانه | 0.9.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Pauline Barbet, Arnaud Felten |
| ایمیل نویسنده | pauline.barbet@anses.fr, arnaud.felten@anses.fr |
| آدرس صفحه اصلی | https://github.com/p-barbet/GENIAL |
| آدرس اینترنتی | https://pypi.org/project/GENIALbiologists/ |
| مجوز | - |
GENIAL : GENes Identification with Abricate for Lucky biologists
================================================================
Authors : Barbet Pauline, Felten Arnaud
Affiliation: [Food Safety Laboratory - ANSES Maisons Alfort (France)](https://www.anses.fr/en/content/laboratory-food-safety-maisons-alfort-and-boulogne-sur-mer)
You can find the latest version of the tool at [https://github.com/p-barbet/GENIAL](https://github.com/p-barbet/GENIAL)
GENIAL
======
GENIAL aims to identify antimicrobial resistance and virulence genes from bacterial genomes matching them to a database gathering genes of interest using [ABRicate](https://github.com/tseemann/abricate).
### Databases
Default databases available are ([Resfinder](https://cge.cbs.dtu.dk/services/ResFinder/), [CARD](https://card.mcmaster.ca/), [ARG-ANNOT](http://backup.mediterranee-infection.com/article.php?laref=282&titre=arg-annot), [NCBI](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047), [EcOH](https://github.com/katholt/srst2/tree/master/data), [PlasmidFinder](https://cge.cbs.dtu.dk/services/PlasmidFinder/), [Ecoli_VF](https://github.com/phac-nml/ecoli_vf) and [VFDB](http://www.mgc.ac.cn/VFs/))
As well as this databes, it's posible to use your own database.
The tool is divided into two scripts.
### GENIALanalysis
GENIALanalysis aims to run ABricate. It takes in input a tsv file containing genomes fasta files paths and IDs.If you want to use your own database you also need to provide a multifasta whith genes IDs as headers. Then the script run ABricate and produce in output one ABRicate result file per genome, corresponding to a tsv file including genes found in each sample.
### GENIALresults
GENIALresults aims to conditionning ABRicate results in the form of matrixes and heatmaps of presence/absence. It takes in input a temporary file produced by the Abricate analysis containing the genomes Abricate results paths and IDs. In the case of vfdb database a file containing the virulence factors names, their family and species is automticaly included in the script.
The output depending on the database used :
* In any cases a matrix in tsv format and a heatmap in png format with all genes found are created
On top of that:
* If you use one of the default databases [Resfinder](https://cge.cbs.dtu.dk/services/ResFinder/) or [VFDB](http://www.mgc.ac.cn/VFs/) news matrix and heatmap by gene type are produced with a correspondace table between the gene name, its family and its number in all genomes.
* If you don't use one of the two previous databases or if you use your own database, only a corespondance table between the gene name and its number in all genomes is produced in addition.
Dependencies
============
The script has been developed with python 3.6 (tested with 3.6.6)
### External dependencies
* [ABRicate](https://github.com/tseemann/abricate) tested with 0.8.7
* [Pandas](https://pandas.pydata.org/) tested with 0.23.4
* [seaborn](https://seaborn.pydata.org/installing.html) tested with 0.9.0
Parameters
==========
### Command line options
| Options | Description | Required | Default |
|:-----------:|:-------------------------------------------------------------------------------------------------------------------------------------:|:----------------------:|:----------------:|
| -f | tsv file with FASTA files paths ans strains IDs | Yes | |
| -dbp | Path to ABRicate databases repertory. Implies -dbf and --privatedb | Yes if --privatedb | |
| -dbf | Multifasta containing the private database sequences. Implies -dbp and --privatedb | Yes if --privatedb | |
| -T | Number of thread to use | No | 1 |
| -w | Working directory | No | . |
| -r | Results directory name | No | ABRicate_results |
| --defaultdb | default databases available : resfinder, card, argannot, acoh, ecoli_vf, plasmidfinder, vfdb or ncbi. Incompatible with --privatedb | Yes if not --privatedb | |
| --privatedb | Private database name. Implies -dbp and -dbf. Incompatible with --defaultdb | Yes if not --defaultdb | |
| --mincov | Minimum proportion of gene covered | No | 80 |
| --minid | Minimum proportion of exact nucleotide matches | No | 90 |
| --R | Remove genes present in all genomes from the matrix | No | False |
Test
====
After installing ABRicate and Pandas and seaborn you can test the script with the command line :
## Default database
python AntiViruce.py -f input_file.tsv --defaultdb vfdb -r results_directory --minid 90 --mincov 80
## Private database
python AntiViruce.py -f input_file.tsv --privatedb private_db_name -T 10 -r results_directory --minid 90 --mincov 80 -dbp path_to_abricate_databases_repertory -dbf private_db_multifasta_path
نیازمندی
| مقدار | نام |
|---|---|
| - | pandas |
| - | seaborn |
| - | biopython |
نحوه نصب
نصب پکیج whl GENIALbiologists-0.9.0:
pip install GENIALbiologists-0.9.0.whl
نصب پکیج tar.gz GENIALbiologists-0.9.0:
pip install GENIALbiologists-0.9.0.tar.gz