# Likelihood Module

<a id="geniml.likelihood.build_model"></a>

<a id="geniml.likelihood.build_model.model_binomial"></a>

## `model_binomial`

```python
def model_binomial(folder_in, in_file, chrom, file_out, file_no=None)
```

Create binomial likelihood model
first column - likelihood of background
second column - likelihood of coverage

<a id="geniml.likelihood.build_model.ChromosomeModel"></a>

## `ChromosomeModel`

```python
class ChromosomeModel(folder, chrom)
```

Args:
    folder: file with the model
    chrom: of which chromosome is the model

### Attributes

- <a id="geniml.likelihood.build_model.ChromosomeModel.folder"></a>**`folder`**
- <a id="geniml.likelihood.build_model.ChromosomeModel.chromosome"></a>**`chromosome`**
- <a id="geniml.likelihood.build_model.ChromosomeModel.start_file"></a>**`start_file`**
- <a id="geniml.likelihood.build_model.ChromosomeModel.core_file"></a>**`core_file`**
- <a id="geniml.likelihood.build_model.ChromosomeModel.end_file"></a>**`end_file`**
- <a id="geniml.likelihood.build_model.ChromosomeModel.files"></a>**`files`**
- <a id="geniml.likelihood.build_model.ChromosomeModel.models"></a>**`models`**

### Methods

<a id="geniml.likelihood.build_model.ChromosomeModel.make_model"></a>

#### `make_model`

```python
def make_model(coverage_folder, coverage_prefix, file_no)
```

Make a lh model of given chromosome from coverage files

Args:
    coverage_folder: path to name with coverage files
    coverage_prefix: prefixed used for making coverage files
    file_no: number of files from which model is being created

<a id="geniml.likelihood.build_model.ChromosomeModel.read"></a>

#### `read`

```python
def read()
```

Read model.

<a id="geniml.likelihood.build_model.ChromosomeModel.read_track"></a>

#### `read_track`

```python
def read_track(track)
```

Read specific track from model.

<a id="geniml.likelihood.build_model.ModelLH"></a>

## `ModelLH`

```python
class ModelLH(file)
```

Likelihood model class

Args:
    file: file containing the model

### Attributes

- <a id="geniml.likelihood.build_model.ModelLH.name"></a>**`name`**
- <a id="geniml.likelihood.build_model.ModelLH.chromosomes_list"></a>**`chromosomes_list`**
- <a id="geniml.likelihood.build_model.ModelLH.chromosomes_models"></a>**`chromosomes_models`**

### Methods

<a id="geniml.likelihood.build_model.ModelLH.make"></a>

#### `make`

```python
def make(coverage_folder, coverage_prefix, file_no, force=False)
```

Make lh model for all chromosomes

Args:
    coverage_folder: folder with coverage files
    coverage_prefix: prefixed used for making coverage files
    file_no: number of file from which model is being made
    force: if overwrite an existing model

<a id="geniml.likelihood.build_model.ModelLH.read_chrom"></a>

#### `read_chrom`

```python
def read_chrom(chrom)
```

Read into model specific chromosome.

<a id="geniml.likelihood.build_model.ModelLH.read_chrom_track"></a>

#### `read_chrom_track`

```python
def read_chrom_track(chrom, track)
```

Read into model specific track for chromosome.

<a id="geniml.likelihood.build_model.ModelLH.clear_chrom"></a>

#### `clear_chrom`

```python
def clear_chrom(chrom)
```

Clear model for given chromosome.

<a id="geniml.likelihood.build_model.main"></a>

## `main`

```python
def main(model_file, coverage_folder, coverage_prefix, file_no=None, force=False)
```

Crate likelihood models for all chromosomes

Args:
    model_file: output name
    coverage_folder: folder with coverage files
    coverage_prefix: prefix used for making coverage files
    file_no: number of files used for making coverage tracks