### Install Development Requirements

Source: https://pypi.org/project/MobileElementFinder

Installs dependencies required for local development.

```bash
pip install -r requirements-devel.txt
```

--------------------------------

### Install MobileElementFinder via PyPI

Source: https://pypi.org/project/MobileElementFinder

Install the MobileElementFinder package and its database using pip.

```bash
$ pip install MobileElementFinder
```

--------------------------------

### Install BLAST via Homebrew

Source: https://pypi.org/project/MobileElementFinder

Install the required NCBI BLAST dependency on macOS using Homebrew.

```bash
$ brew install blast
```

--------------------------------

### Update MobileElementFinder

Source: https://pypi.org/project/MobileElementFinder

Updates the local installation of MobileElementFinder using pip.

```bash
pip install -e . --upgrade
```

--------------------------------

### MobileElementFinder CLI Help

Source: https://pypi.org/project/MobileElementFinder

View the full list of available command-line options and configuration flags.

```text
Usage: mobileElementFinder.py find [OPTIONS] OUTPUT

  Find mobile element in sequence data.

Options:
  -c, --contig PATH        Specify pre-assembled contigs to perform analysis
                           on.

  -f, --fq-file PATH       Sequencing files in fastq format. Only used for
                           annotating sequence depth in GFF files (Optional)

  --config FILE            Path to user defined config
  -j, --json               Write output in json format.
  -g, --gff                Write MGE location on contig in gff format.
  -t, --threads INTEGER    Number of threads [default: 1]
  --min-coverage FLOAT     Minimum coverage
  --max-evalue INTEGER     Maximum alignment e-value
  --temp-dir PATH          Set directory for temporary files.
  --kma-path TEXT          Path to KMA, if the executable is not in PATH
  --blastn-path TEXT       Path to Blast, if the executable is not in PATH
  --makeblastdb-path TEXT  Path to Blast, if the executable is not in PATH
  --db-path PATH           Path to MGEdb
  --help                   Show this message and exit.
```

--------------------------------

### Run MobileElementFinder via Docker

Source: https://pypi.org/project/MobileElementFinder

Executes the tool using a make command that forwards arguments to the container.

```bash
$ make run CMD="mefinder find -t 4 -f ./data/forward_reads.fastq -f ./data/reverse_reads.fastq result"
```

--------------------------------

### Run MobileElementFinder Analysis

Source: https://pypi.org/project/MobileElementFinder

Execute the find command to analyze assembled contigs and generate output files.

```bash
$ mefinder find --contig /path/to/genome.fna output_name
```

--------------------------------

### Run Integration Tests

Source: https://pypi.org/project/MobileElementFinder

Executes automated integration tests for specific Python versions using tox.

```bash
tox py37 py38
```

--------------------------------

### Pull Docker Images

Source: https://pypi.org/project/MobileElementFinder

Downloads pre-built Docker images for MobileElementFinder from Dockerhub.

```bash
# pull the latest build
$ docker pull mkhj/mobile_element_finder:latest

# pull version 1.0.5
$ docker pull mkhj/mobile_element_finder:1.0.5
```

--------------------------------

### Access Container Interactively

Source: https://pypi.org/project/MobileElementFinder

Opens a bash shell inside the MobileElementFinder Docker container.

```bash
$ make bash
```

--------------------------------

### Lint Code

Source: https://pypi.org/project/MobileElementFinder

Runs code linting using tox.

```bash
tox lint
```

--------------------------------

### mefinder find

Source: https://pypi.org/project/MobileElementFinder

The primary command to find mobile elements in sequence data. It requires a contig file as input and an output name for the generated files.

```APIDOC
## mefinder find

### Description
Find mobile elements in sequence data using assembled contigs.

### Parameters
#### Options
- **--contig** (PATH) - Required - Specify pre-assembled contigs to perform analysis on.
- **--fq-file** (PATH) - Optional - Sequencing files in fastq format for annotating sequence depth.
- **--config** (FILE) - Optional - Path to user defined config.
- **--json** (FLAG) - Optional - Write output in json format.
- **--gff** (FLAG) - Optional - Write MGE location on contig in gff format.
- **--threads** (INTEGER) - Optional - Number of threads [default: 1].
- **--min-coverage** (FLOAT) - Optional - Minimum coverage.
- **--max-evalue** (INTEGER) - Optional - Maximum alignment e-value.
- **--temp-dir** (PATH) - Optional - Set directory for temporary files.
- **--kma-path** (TEXT) - Optional - Path to KMA, if the executable is not in PATH.
- **--blastn-path** (TEXT) - Optional - Path to Blast, if the executable is not in PATH.
- **--makeblastdb-path** (TEXT) - Optional - Path to Blast, if the executable is not in PATH.
- **--db-path** (PATH) - Optional - Path to MGEdb.
```

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