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https://github.com/ikergarcia1996/gene2tab
This script is used to convert the output of ABRICATE tabulated output into a matrix samples with the genes as columns and the presence/absence of the gene as the values.
https://github.com/ikergarcia1996/gene2tab
abricate genomic-data-analysis genomics genomics-visualization table
Last synced: 7 days ago
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This script is used to convert the output of ABRICATE tabulated output into a matrix samples with the genes as columns and the presence/absence of the gene as the values.
- Host: GitHub
- URL: https://github.com/ikergarcia1996/gene2tab
- Owner: ikergarcia1996
- License: apache-2.0
- Created: 2023-11-17T16:07:59.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2023-11-18T11:01:07.000Z (about 1 year ago)
- Last Synced: 2024-12-22T05:13:06.329Z (27 days ago)
- Topics: abricate, genomic-data-analysis, genomics, genomics-visualization, table
- Language: Python
- Homepage: https://pypi.org/project/gene2tab
- Size: 28.3 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Gene2Tab
## Description
This script is used to convert the output of [ABRICATE](https://github.com/tseemann/abricate) tabulated output into a matrix samples with the genes as columns and the presence/absence of the gene as the values.
The script can use as input a directory containing multiple `.tab` files or a single `.tab` file. The output will be a `.csv` file. Each file should contain the `#File` `Sequence` and `GENE` columns, the other ones are optional.
By default, **the script will only consider genes with a coverage and identity of 90% or more**. This can be changed with the `--min_coverage` and `--min_identity` flags.
Example:
File1.tab
```tsv
#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE
Isolate1 S1-length_513 53228 54445 + ceoA 1-1218/1218 ========/====== 2/2 99.92 99.67 card U97042:0-1218 ceoA is a periplasmic linker subunit of the CeoAB-OpcM efflux pump aminoglycoside;fluoroquinolone
Isolate1 S1-length_513 54491 57575 + ceoB 1-3084/3084 ========/====== 1/1 100 99.87 card U97042:1263-4347 ceoB is a cytoplasmic membrane component of the CeoAB-OpcM efflux pump aminoglycoside;fluoroquinolone
Isolate1 S1-length_513 57702 59240 + opcM 1-1536/1536 ========/====== 5/5 99.93 99.16 card U38944.1:0-1536 OpcM is an outer membrane factor protein found in Burkholderia cepacia. It is part of the CeoAB-OpcM complex. aminoglycoside;fluoroquinolone
Isolate1 S1-length_233 145199 146378 + amrA 24-1200/1200 ========/====== 15/23 97.25 80.84 card BX571965.1:2152165-2150965 amrA is the efflux pump subunit of the AmrAB-OprM multidrug efflux complex. amrA corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. aminoglycoside
Isolate1 S1-length_233 146394 149503 + amrB 1-3110/3132 ========/====== 2/2 99.27 88.17 card BX571965.1:2150949-2147817 amrB is the membrane fusion protein of the AmrAB-OprM multidrug efflux complex. aminoglycoside
Isolate1 S1-length_265 25329 26405 + Burkholderia_pseudomallei_Omp38 1-1122/1122 ========/====== 14/59 95.37 80.78 card AY312416:0-1122 Heterologous expression of Burkholderia pseudomallei Omp38 (BpsOmp38) in Omp-deficient E. coli host cells lowers their permeability and in consequence their antimicrobial susceptibility to penicillin G cefoxitin ceftazidime and imipenem. carbapenem;cephalosporin;cephamycin;monobactam;penam;penem
Isolate2 S2-length_512 25329 26405 + Burkholderia_pseudomallei_Omp38 1-1122/1122 ========/====== 14/59 95.37 80.78 card AY312416:0-1122 Heterologous expression of Burkholderia pseudomallei Omp38 (BpsOmp38) in Omp-deficient E. coli host cells lowers their permeability and in consequence their antimicrobial susceptibility to penicillin G cefoxitin ceftazidime and imipenem. carbapenem;cephalosporin;cephamycin;monobactam;penam;penem
```
File2.tab
```tsv
#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE
Isolate2 S2-length_512 25329 26405 + Burkholderia_pseudomallei_Omp38 1-1122/1122 ========/====== 14/59 95.37 80.78 card AY312416:0-1122 Heterologous expression of Burkholderia pseudomallei Omp38 (BpsOmp38) in Omp-deficient E. coli host cells lowers their permeability and in consequence their antimicrobial susceptibility to penicillin G cefoxitin ceftazidime and imipenem. carbapenem;cephalosporin;cephamycin;monobactam;penam;penem
```
Will be converted to:
```csv
Sample,ceoA,ceoB,opcM,amrA,amrB,Burkholderia_pseudomallei_Omp38
BUR-BAB-IMI-102146,1,1,1,1,1,1
AA2,0,0,0,0,0,1
```
If the `--transpose` flag is used, the output will be:
```csv
Sample,Isolate1,Isolate2
ceoA,1,0
ceoB,1,0
opcM,1,0
amrA,1,0
amrB,1,0
Burkholderia_pseudomallei_Omp38,1,1
```
## Installation
```bash
pip install gene2tab
```
## Usage
See all the available options with:
```bash
gene2tab -h
```
Running the script. The input can be a single `.tab` file or a directory containing multiple `.tab` files. The output will be a `.csv` file.
```bash
gene2tab -i [output_directory or file.tab] -o output.csv --min_coverage 0.9 --min_identity 0.9
```
You can also transpose the output with the `--transpose` flag.
```bash
gene2tab -i [output_directory or file.tab] -o output.csv --min_coverage 0.9 --min_identity 0.9 --transpose
```
If your files use a different delimiter than tab, you can specify it with the `--input_file_delimiter` flag.
```bash
gene2tab -i [output_directory or file.tab] -o output.csv --min_coverage 0.9 --min_identity 0.9 --input_file_delimiter ','
```
If you want a different delimiter in the output file, you can specify it with the `--output_file_delimiter` flag.
```bash
gene2tab -i [output_directory or file.tab] -o output.csv --min_coverage 0.9 --min_identity 0.9 --output_delimiter ';'
```
## License
Apache License 2.0