Metadata-Version: 2.1
Name: bfscan
Version: 0.0.2
Summary: bfscan is designed to detect foodborne pathogens using bloom filter and machine learning
Author: Thiago Pereira de Oliveira Carvalho, Frederico Schmitt Kremer
Author-email: thg.baum@gmail.com, fred.s.kremer@gmail.com
License: UNKNOWN
Keywords: bioinformatics bloom filter data science foodborne pathogen
Platform: UNKNOWN
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas
Requires-Dist: Biopython
Requires-Dist: tqdm
Requires-Dist: numpy
Requires-Dist: bloom-filter2
Requires-Dist: scikit-learn
Requires-Dist: imbalanced-learn
Requires-Dist: twine

# bfscan

BFScan is a tool to scan FASTA and FASTQ files using a combination of
k-mer composition, Bloom-filter and machine learning methods. 

## Example

### 1. Construction a collection of Bloom filters for targets organisms

```
$ bfscan-build-filters \
    -i \
        data/fasta/salmonella.fasta \
        data/fasta/listeria.fasta \
        data/fasta/campylobacter.fasta
    -o data/filters/filter
```

### 2. Training a machine learning model

```
$ bfscan-build-model \
    -i \
        data/fasta/salmonella.fasta \
        data/fasta/listeria.fasta \
        data/fasta/campylobacter.fasta
    -o data/models/model \
    -background data/fastq/metagenome.fastq \
    -r data/reports/classification_report.txt
```

### 3. Running the search

```
$ bfscan-search \
    -i \
        reads.fastq
    -o data/results/filtered \
    -F fastq
``


