restidy

Introduction

Restidy is write to process and tidy the AMR results after using ResFinder4.0

You will get the following results after using ResFinder4.0.

Sample01
├── PointFinder_prediction.txt
├── PointFinder_results.txt
├── PointFinder_table.txt
├── ResFinder_Hit_in_genome_seq.fsa
├── ResFinder_Resistance_gene_seq.fsa
├── ResFinder_results.txt
├── ResFinder_results_tab.txt
├── ResFinder_results_table.txt
├── pheno_table.txt
├── pheno_table_salmonella.txt
├── pointfinder_blast

Here are the content in ResFinder_results_tab.txt and PointFinder_results.txt files, which were mainly used as input data by restidy.

ResFinder_results_tab.txt

Resistance gene	Identity	Alignment Length/Gene Length	Coverage	Position in reference	Contig	Position in contig	Phenotype	Accession no.
aac(6')-Iaa	99.32	438/438	100.0	1..438	contig1_denovo_ah19S2	164272..164709	Aminoglycoside resistance	NC_003197
qnrS1	100.00	657/657	100.0	1..657	contig26_denovo_ah19S2	7634..8290	Quinolone resistance	AB187515

PointFinder_results.txt

Mutation	Nucleotide change	Amino acid change	Resistance	PMID
parC p.T57S	ACC -> AGC	T -> S	Nalidixic acid,Ciprofloxacin	15388468

After using restidy, you will get the following results:

output
├── drug_pivot.csv # Pivot table of AMR corresponding drugs
├── pattern_process.csv # AMR and Drugs profile pattern
├── point_sum.csv # The summary of PointFinder result in pivot style
├── resfinder_sum.csv # The summary of ResFinder result in pivot style
└── resistance_statistic.csv # The number of isolates resistance to found drugs.

Installation

Using pip:

pip3 install restidy==0.2.8

You could run the following command to run a test to check if restidy have been correctly installed.

restidy -i PATH_TO/demo_data -o OUTPUT_DIR

Usage

usage: restidy -i < resfinder4.0_result_directory > -o < output_file_directory >

Author: Qingpo Cui(SZQ Lab, China Agricultural University)

optional arguments:
  -h, --help     show this help message and exit
  -i I           <input_path>: resfinder_result_path
  -o O           <output_file_path>: output_file_path
  -p P           True of False to process point mutation results
  -v, --version  Display version