https://github.com/mrzresearcharena/card-rgi
https://github.com/mrzresearcharena/card-rgi
Last synced: 2 months ago
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- Host: GitHub
- URL: https://github.com/mrzresearcharena/card-rgi
- Owner: mrzResearchArena
- Created: 2019-01-24T07:14:51.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-07-24T20:26:57.000Z (almost 6 years ago)
- Last Synced: 2025-01-16T12:55:13.244Z (4 months ago)
- Language: Python
- Size: 1.17 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Resistance Gene Identifier (RGI) for E. coli (Bacteria)
## Code Description
### 1. Generate Datasets (JSON)
##### Step 1.1: Basic Process [ [Generate Datasets](https://github.com/mrzResearchArena/CARD-RGI/blob/master/generateDatasets.py) ]
##### Step 1.2: Parallel Processing [ [Generate Datasets](https://github.com/mrzResearchArena/CARD-RGI/blob/master/generateDatasetsParallelProcessing.py) ]
`Note: The programme will take FASTA sequences as inputs; it will produce JSON file for each sequence.`
### 2. HeatMap:
##### Step 2.1 Heatmap [ [HeatMap](https://github.com/mrzResearchArena/CARD-RGI/blob/master/heatMap.py) ]
`Note: The programme will take previously generated JSON file as inputs; it will produce heatmap.`
### 3. Generate Datasets (CSV)
##### Step 3.1 [ [Generate Percentage CSV](https://github.com/mrzResearchArena/CARD-RGI/blob/master/WriteCSV.py) ]
##### Step 3.2 [ [Generate Binary CSV](https://github.com/mrzResearchArena/CARD-RGI/blob/master/WriteCSV_binary.py) ]
`Note: The programme will take previously generated JSON file as inputs; it will produce the name of antibiotic resistance ontology (ARO) and the percentage of identity for each ARO.`
##### Step 3.3 Visualize Datasets
Please [click here](https://github.com/mrzResearchArena/CARD-RGI/blob/master/output.csv) to visualize the CSV file (percentage).
Please [click here](https://github.com/mrzResearchArena/CARD-RGI/blob/master/binaryOutput.csv) to visualize the CSV file (binary).
### 4. Dendrogram with HeatMap:
##### Step 4.1 [ [Draw Dendrogram HeatMap](https://github.com/mrzResearchArena/CARD-RGI/blob/master/dendrogramHeatMap.py) ]
`Note: The programme will take previously generated CSV file as input; it will produce dendrogram with heatmap.`
## HeatMap ( Command-line )
#### Step 1: Default
```console
rafsanjani@mrz:~$ rgi heatmap --input PATH
```
#### Step 2: Gene Family
```console
rafsanjani@mrz:~$ rgi heatmap --input PATH --category gene_family --display text
```
#### Step 3: Profile Frequency
```console
rafsanjani@mrz:~$ rgi heatmap --input PATH --frequency
```
#### Step 3: Drug Class Frequency
```console
rafsanjani@mrz:~$ rgi heatmap --input PATH --category drug_class --frequency --display text
```
#### Step 4: Cluster
##### Step 4.1: Default Cluster
```console
rafsanjani@mrz:~$ rgi heatmap --input PATH --cluster both
```
##### Step 4.2: Cluster on Resistance Mechanism
```console
rafsanjani@mrz:~$ rgi heatmap --input PATH --cluster samples --category resistance_mechanism --display text
```
## Heatmap ( Image )
##### Gene Family RGI Heatap
##### Profile Frequency RGI Heatmap
##### Drug Class Frequency RGI Heatmap
##### Cluster RGI Heatmap
##### Cluster Resistance Mechanism RGI Heatmap
## Dendrogram with Heatmap ( Image )
##### Dendrogram with Heatmap
## Color Code
- Yellow represents a perfect hit,
- Teal represents a strict hit,
- Purple represents no hit.