### Install PyHMMER and Run Tests

Source: https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md

Install the extension locally in editable mode and run Python unit tests. Ensure no build isolation for proper installation.

```bash
python -m pip install -e . -v --no-build-isolation
python -m unittest pyhmmer.tests -vv
```

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

### Install PyHMMER for Benchmarking

Source: https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md

Install the extension in release mode for running benchmarks. This requires HMMER binaries in PATH and the 'hyperfine' tool.

```bash
python -m pip install . -v --no-build-isolation
```

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

### Install and Run PyHMMER Tests

Source: https://github.com/althonos/pyhmmer/blob/master/docs/guide/contributing.md

Install the extension locally in editable mode and run unit tests using the unittest module. Requires the extension to be built.

```bash
$ python -m pip install -e . -v --no-build-isolation
$ python -m unittest pyhmmer.tests -vv
```

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

### Install pyhmmer using pip

Source: https://github.com/althonos/pyhmmer/blob/master/README.md

Install pyhmmer from PyPI using pip. This command installs pre-built wheels for Linux and MacOS or compiles from source with Cython.

```console
pip install pyhmmer
```

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

### Build and Install PyHMMER from GitHub source

Source: https://github.com/althonos/pyhmmer/blob/master/docs/guide/install.md

Clone the pyhmmer repository from GitHub and build/install it manually using the 'build' and 'installer' tools.

```console
$ git clone --recursive https://github.com/althonos/pyhmmer
$ cd pyhmmer
$ python -m build .
# python -m installer dist/*.whl
```

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

### Project and Language Setup

Source: https://github.com/althonos/pyhmmer/blob/master/CMakeLists.txt

Initializes the CMake project, specifying the minimum version, project name, version, and programming languages.

```cmake
cmake_minimum_required(VERSION 3.20)
project(${SKBUILD_PROJECT_NAME} VERSION ${SKBUILD_PROJECT_VERSION} LANGUAGES C)
```

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

### Installing Shared Libraries and Headers

Source: https://github.com/althonos/pyhmmer/blob/master/src/easel/CMakeLists.txt

Installs the 'libeasel' library and its header files if PYHMMER_INSTALL_LIBS_DIR is defined. Sets runtime path properties for shared libraries on macOS and other Unix-like systems.

```cmake
if(DEFINED PYHMMER_INSTALL_LIBS_DIR)
    install(TARGETS libeasel DESTINATION "${SKBUILD_PLATLIB_DIR}/${PYHMMER_INSTALL_LIBS_DIR}")
    if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
        set_target_properties(libeasel PROPERTIES INSTALL_RPATH "@loader_path/")
    else()
        set_target_properties(libeasel PROPERTIES INSTALL_RPATH "$ORIGIN/")
    endif()
    cmake_path(APPEND SKBUILD_PLATLIB_DIR "${PYHMMER_INSTALL_LIBS_DIR}" "include" "libeasel" OUTPUT_VARIABLE INCLUDE_DEST_FOLDER)
    foreach(_file IN ITEMS ${EASEL_PATCHED_SOURCES})
        cmake_path(GET _file EXTENSION LAST_ONLY _ext)
        if(_ext STREQUAL ".h")
            cmake_path(RELATIVE_PATH _file BASE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" OUTPUT_VARIABLE _local)
            cmake_path(GET _local PARENT_PATH _dest)
            install(FILES "${_file}" DESTINATION "${INCLUDE_DEST_FOLDER}/${_dest}")
        endif()
    endforeach()
  endif()
```

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

### Install PyHMMER from GitHub using pip

Source: https://github.com/althonos/pyhmmer/blob/master/docs/guide/install.md

Install the latest version of pyhmmer directly from its GitHub repository using pip.

```console
$ pip install -U git+https://github.com/althonos/pyhmmer
```

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

### Install CMake Package Configuration Files

Source: https://github.com/althonos/pyhmmer/blob/master/src/cmake/CMakeLists.txt

Installs the generated CMake configuration files to the package's installation directory. This makes the package discoverable by other CMake projects.

```cmake
install(
    FILES
    ${CMAKE_CURRENT_BINARY_DIR}/PyHMMERConfigVersion.cmake
    ${CMAKE_CURRENT_BINARY_DIR}/PyHMMERConfig.cmake
    DESTINATION ${PYHMMER_INSTALL_LIBS_DIR}/cmake/PyHMMER
)
```

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

### Install PyHMMER from piwheels

Source: https://github.com/althonos/pyhmmer/blob/master/docs/guide/install.md

Install pyhmmer from piwheels.org, which provides pre-built wheels for Raspberry Pi computers.

```console
$ pip3 install pyhmmer --extra-index-url https://www.piwheels.org/simple
```

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

### Configure setuptools to include HMM files

Source: https://github.com/althonos/pyhmmer/blob/master/docs/examples/embed_hmms.md

This configuration tells `setuptools` to include all files with the `.hmm` extension from the `redox_detector` package directory into the distribution files. This ensures HMMs are installed alongside your package.

```INI
[options.package_data]
redox_detector = *.hmm
```

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

### Install PyHMMER using pacman on BioArchLinux

Source: https://github.com/althonos/pyhmmer/blob/master/docs/guide/install.md

Install pyhmmer from the BioArchLinux repository using pacman after adding the repository to pacman.conf.

```ini
[bioarchlinux]
Server = https://repo.bioarchlinux.org/$arch
```

```console
$ pacman -Sy
$ pacman -S python-pyhmmer
```

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

### Installing Platform-Specific Header Files

Source: https://github.com/althonos/pyhmmer/blob/master/src/pyhmmer/platform/CMakeLists.txt

Installs header files ('linux.h', 'bsd.h', 'util.h') to a specified include directory if the PYHMMER_INSTALL_LIBS_DIR variable is defined. This is used for platform-specific include paths.

```cmake
if(DEFINED PYHMMER_INSTALL_LIBS_DIR)
    cmake_path(APPEND SKBUILD_PLATLIB_DIR "${PYHMMER_INSTALL_LIBS_DIR}" "include" "pyhmmer" "platform" OUTPUT_VARIABLE INCLUDE_DEST_FOLDER)
    install(FILES "linux.h" "bsd.h" "util.h" DESTINATION "${INCLUDE_DEST_FOLDER}")
endif()
```

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

### Include Folder Setup

Source: https://github.com/althonos/pyhmmer/blob/master/CMakeLists.txt

Defines the directory for Cython headers. This is used to ensure that generated header files are found during the build process.

```cmake
set(CYTHON_HEADERS_DIR ${CMAKE_CURRENT_LIST_DIR}/include)
```

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

### Install PyHMMER using AUR helper (aura)

Source: https://github.com/althonos/pyhmmer/blob/master/docs/guide/install.md

Install the python-pyhmmer package from the Arch User Repository using the 'aura' AUR helper.

```console
$ aura -A python-pyhmmer
```

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

### Run Benchmarks

Source: https://github.com/althonos/pyhmmer/blob/master/docs/guide/contributing.md

Execute the benchmark suite using the provided UNIX shell script. Assumes HMMER binaries and 'hyperfine' are in the PATH and the extension is installed.

```bash
$ ./benches/run.sh
```

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

### Run Benchmarks

Source: https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md

Execute the benchmark suite using the provided shell script. This assumes the PyHMMER extension is installed and dependencies are met.

```bash
./benches/run.sh
```

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

### Install Shared Libraries and Headers

Source: https://github.com/althonos/pyhmmer/blob/master/src/hmmer/CMakeLists.txt

This conditional block handles the installation of the 'libhmmer' library and its headers if the 'PYHMMER_INSTALL_LIBS_DIR' variable is defined. It sets the runtime path for shared libraries on macOS and other systems.

```cmake
if(DEFINED PYHMMER_INSTALL_LIBS_DIR)
    install(TARGETS libhmmer DESTINATION "${SKBUILD_PLATLIB_DIR}/${PYHMMER_INSTALL_LIBS_DIR}")
    if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
        set_target_properties(libhmmer PROPERTIES INSTALL_RPATH "@loader_path/")
    else()
        set_target_properties(libhmmer PROPERTIES INSTALL_RPATH "$ORIGIN/")
    endif()
    cmake_path(APPEND SKBUILD_PLATLIB_DIR "${PYHMMER_INSTALL_LIBS_DIR}" "include" "libhmmer" OUTPUT_VARIABLE INCLUDE_DEST_FOLDER)
    foreach(_file IN ITEMS ${HMMER_PATCHED_SOURCES})
        cmake_path(GET _file EXTENSION LAST_ONLY _ext)
        if(_ext STREQUAL ".h")
            cmake_path(RELATIVE_PATH _file BASE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" OUTPUT_VARIABLE _local)
            cmake_path(GET _local PARENT_PATH _dest)
            install(FILES "${_file}" DESTINATION "${INCLUDE_DEST_FOLDER}/${_dest}")
        endif()
    endforeach()
endif()
```

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

### Import PyHMMER and Check Version

Source: https://github.com/althonos/pyhmmer/blob/master/docs/examples/msa_to_hmm.ipynb

Imports the pyhmmer library and displays its version. Ensure pyhmmer is installed.

```python
import pyhmmer
pyhmmer.__version__
```

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

### Running a HMM Search with a Bitscore Cutoff

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/hmmer/profile.md

Example of how to run `hmmsearch` using a bitscore cutoff (T=5) instead of the default E-value cutoff. This requires passing the `T` keyword argument.

```python
>>> hits = next(hmmsearch(thioesterase, proteins, T=5))
>>> hits[0].score
8.601...
```

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

### Match Emissions Example

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/hmms.md

Illustrates the structure of the match emissions matrix. The first row corresponds to entry probabilities and is conventionally set with 1 probability for the first symbol.

```python
>>> hmm = HMM(easel.Alphabet.dna(), 100, "test")
>>> hmm.match_emissions
MatrixF([[1.0, 0.0, 0.0, 0.0], ...])
```

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

### Install pyhmmer using conda

Source: https://github.com/althonos/pyhmmer/blob/master/README.md

Install pyhmmer from the bioconda channel using conda. This is an alternative installation method for users of the conda package manager.

```console
conda install -c bioconda pyhmmer
```

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

### Initialize and Search with Pipeline

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/results.md

Demonstrates initializing a Pipeline and performing a search to obtain TopHits. Shows how to check if the results are sorted by key.

```default
>>> abc = thioesterase.alphabet
>>> hits = Pipeline(abc).search_hmm(thioesterase, proteins)
>>> hits.is_sorted(by="key")
True
```

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

### Initialize and Configure Plan7 Builder

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/pli.md

Demonstrates initializing a Plan7 Builder with a specific alphabet and background, setting the score matrix, and then building an HMM from a protein sequence.

```python
alphabet = easel.Alphabet.amino()
background = plan7.Background(alphabet)
builder = plan7.Builder(alphabet, popen=0.05)
builder.score_matrix = "BLOSUM90"
hmm, _, _ = builder.build(proteins[0], background)
```

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

### Client Initialization and Connection

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/daemon/client.md

Instantiate a Client and establish a connection to the HMMER daemon server. The client can also be used as a context manager.

```APIDOC
## Client

### *class* pyhmmer.daemon.Client

A `socket`-based client to communicate with a HMMER daemon server.

This class implements the client-side protocol to query a database with
a [`Sequence`](../easel/seq.md#pyhmmer.easel.Sequence), [`MSA`](../easel/msa.md#pyhmmer.easel.MSA) or [`HMM`](../plan7/hmms.md#pyhmmer.plan7.HMM).
It must first connect to the server with the [`connect`](#pyhmmer.daemon.Client.connect) method:

```default
>>> client = daemon.Client("127.0.0.1", 51371)
>>> client.connect()
```

Afterwards, the client can be used to run pipelined searches,
returning a [`TopHits`](../plan7/results.md#pyhmmer.plan7.TopHits):

```default
>>> client.search_hmm(thioesterase)
<pyhmmer.plan7.TopHits object at 0x...>
```

Additional keyword arguments can be passed to customize the pipelined
search. All parameters from [`Pipeline`](../plan7/pli.md#pyhmmer.plan7.Pipeline) are supported:

```default
>>> client.search_hmm(thioesterase, F1=0.02, E=1e-5)
<pyhmmer.plan7.TopHits object at 0x...>
```

#### HINT
[`Client`](#pyhmmer.daemon.Client) implements the context manager protocol, which can be used
to open and close a connection to the server within a context:

```default
>>> with daemon.Client() as client:
...    client.search_hmm(thioesterase)
<pyhmmer.plan7.TopHits object at 0x...>
```

#### Versionadded
Added in version 0.6.0.

#### __init__(address='127.0.0.1', port=51371)

Create a new [`Client`](#pyhmmer.daemon.Client) connecting to the given HMMER daemon server.

* **Parameters:**
  * **address** (`str`) – The address of the HMMER daemon server.
  * **port** (`int`) – The port over which the HMMER daemon server
    performs client/server communication.

#### close()

Close the connection to the HMMER daemon server.

#### connect()

Connect the client to the HMMER daemon server.
```

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

### pyhmmer.plan7.HMM.__init__

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/hmms.md

Creates a new HMM from scratch with a specified alphabet, length, and name.

```APIDOC
## pyhmmer.plan7.HMM.__init__

### Description
Create a new HMM from scratch.

### Method
`__init__(alphabet, M, name)`

### Parameters
#### Parameters
- **alphabet** (`Alphabet`) - The alphabet of the model.
- **M** (`int`) - The length of the model (i.e. the number of nodes).
- **name** (`str`) - The name of the model.
```

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

### __init__

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/misc.md

Creates a new SSI file writer for the specified file location. It can optionally create the file if it doesn't exist.

```APIDOC
## __init__

### Description
Create a new SSI file write for the file at the given location.

### Parameters
#### Path Parameters
* **file** (str, bytes or os.PathLike) – The path to a sequence/subsequence index file to write.
* **exclusive** (bool) – Whether or not to create a file if one does not exist.

### Raises
* **FileNotFoundError** – When the path to the file cannot be resolved.
* **FileExistsError** – When the file exists and `exclusive` is `True`.
```

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

### Pipeline Initialization

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/pli.md

Instantiate and configure a new accelerated comparison pipeline with various biological and statistical parameters.

```APIDOC
## Pipeline(
    alphabet,
    background=None,
    *, 
    bias_filter=True,
    null2=True,
    seed=42,
    Z=None,
    domZ=None,
    F1=0.02,
    F2=0.001,
    F3=1e-05,
    E=10.0,
    T=None,
    domE=10.0,
    domT=None,
    incE=0.01,
    incT=None,
    incdomE=0.01,
    incdomT=None,
    bit_cutoffs=None
)

### Description
Instantiate and configure a new accelerated comparison pipeline.

### Parameters
#### Positional Parameters:
* **alphabet** ([`Alphabet`](../easel/alphabet.md#pyhmmer.easel.Alphabet)) – The biological alphabet of the HMMs and sequences to be compared. Used to build the background model.
* **background** ([`Background`](#pyhmmer.plan7.Background), optional) – The background model to use with the pipeline, or `None` to create and use a default one. The pipeline needs ownership of the background model, so any background model passed will be copied.

#### Keyword Arguments:
* **bias_filter** (`bool`) – Whether or not to enable composition bias filter. Defaults to `True`.
* **null2** (`bool`) – Whether or not to compute biased composition score corrections. Defaults to `True`.
* **seed** (`int`, optional) – The seed for the random number generator. Pass `0` to use a one-time arbitrary seed, or `None` to keep the default seed from HMMER.
* **Z** (`int`, optional) – The effective number of comparisons done, for E-value calculation. Leave as `None` to auto-detect by counting the number of sequences queried.
* **domZ** (`int`, optional) – The number of significant sequences found, for domain E-value calculation. Leave as `None` to auto-detect by counting the number of sequences reported.
* **F1** (`float`) – The MSV filter threshold.
* **F2** (`float`) – The Viterbi filter threshold.
* **F3** (`float`) – The uncorrected Forward filter threshold.
* **E** (`float`) – The per-target E-value threshold for reporting a hit.
* **T** (`float`, optional) – The per-target bit score threshold for reporting a hit. If given, takes precedence over `E`.
* **domE** (`float`) – The per-domain E-value threshold for reporting a domain hit.
* **domT** (`float`, optional) – The per-domain bit score threshold for reporting a domain hit. If given, takes precedence over `domE`.
* **incE** (`float`) – The per-target E-value threshold for including a hit in the resulting [`TopHits`](results.md#pyhmmer.plan7.TopHits).
* **incT** (`float`, optional) – The per-target bit score threshold for including a hit in the resulting [`TopHits`](results.md#pyhmmer.plan7.TopHits). If given, takes precedence over `incE`.
* **incdomE** (`float`) – The per-domain E-value threshold for including a domain in the resulting [`TopHits`](results.md#pyhmmer.plan7.TopHits).
* **incdomT** (`float`, optional) – The per-domain bit score thresholds for including a domain in the resulting [`TopHits`](results.md#pyhmmer.plan7.TopHits). If given, takes precedence over `incdomE`.
* **bit_cutoffs** (`str`, optional) – The model-specific thresholding option to use for reporting hits. With `None` (the default), use global pipeline options; otherwise pass one of `
```

```APIDOC
## Pipeline.arguments()

### Description
Generate an `argv`-like list with pipeline options as CLI flags.

### Versionadded
Added in version 0.6.0.
```

```APIDOC
## Pipeline.clear()

### Description
Reset the pipeline to its default state.
```

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

### Install Shared Libraries

Source: https://github.com/althonos/pyhmmer/blob/master/CMakeLists.txt

Conditionally installs shared library objects to a specific directory (`pyhmmer.libs`) if the `PYHMMER_INSTALL_LIBS` variable is set. This is useful for packaging tools like auditwheel.

```cmake
if(PYHMMER_INSTALL_LIBS)
    set(PYHMMER_INSTALL_LIBS_DIR "${CMAKE_PROJECT_NAME}.libs")
    message(STATUS "Installing shared libraries to ${PYHMMER_INSTALL_LIBS_DIR}")
    install(DIRECTORY "${CYTHON_HEADERS_DIR}" DESTINATION "${PYHMMER_INSTALL_LIBS_DIR}/cython")
endif()
```

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

### Using HMMFile with a context manager

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/parsers.md

Demonstrates how to open and read an HMM from a file using the HMMFile class within a 'with' statement, ensuring automatic resource cleanup.

```python
>>> with HMMFile("tests/data/hmms/bin/Thioesterase.h3m") as hmm_file:
...     hmm = hmm_file.read()
```

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

### to_profile(background=None, L=400, multihit=True, local=True)

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/hmms.md

Creates a new profile configured for this HMM, serving as a shortcut for initializing and configuring a Profile object.

```APIDOC
## to_profile(background=None, L=400, multihit=True, local=True)

### Description
Create a new profile configured for this HMM.

This method is a shortcut for creating a new [`Profile`](#pyhmmer.plan7.Profile) and calling [`configure`](#pyhmmer.plan7.Profile.configure) for a given HMM. Prefer manually calling [`configure`](#pyhmmer.plan7.Profile.configure) to recycle the profile buffer when running inside a loop.

### Parameters
#### Path Parameters
- **background** ([`Background`](pli.md#pyhmmer.plan7.Background), optional) – The null background model. In `None` given, create a default one for the HMM alphabet.
- **L** (`int`) – The expected target sequence length.
- **multihit** (`bool`) – Whether or not to use multihit mode.
- **local** (`bool`) – Whether to use local or global mode.
```

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

### Background.__init__

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/pli.md

Creates a new background model for the given alphabet.

```APIDOC
## Background.__init__(alphabet, uniform=False)

### Description
Create a new background model for the given `alphabet`.

### Parameters
#### Path Parameters
* **alphabet** (`Alphabet`) – The alphabet to create the background model with.
* **uniform** (`bool`) – Whether or not to create the null model with uniform frequencies. Defaults to `False`.

### Method
POST

### Endpoint
/background
```

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

### DigitalSequence.source

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/seq.md

Gets the source of the sequence, if any.

```APIDOC
## DigitalSequence.source

### Description
The source of the sequence, if any.

### Type
`str`

### Versionchanged
Changed in version 0.12.0: Property is now a `str` instead of `bytes`.
```

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

### Building the Easel Library

Source: https://github.com/althonos/pyhmmer/blob/master/src/easel/CMakeLists.txt

Creates a static library named 'libeasel' using the processed source files. It also sets public include directories for the library.

```cmake
add_library(libeasel ${EASEL_PATCHED_SOURCES})
target_include_directories(libeasel PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
target_include_directories(libeasel PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
```

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

### DigitalSequence.name

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/seq.md

Gets the name of the sequence.

```APIDOC
## DigitalSequence.name

### Description
The name of the sequence.

### Type
`str`

### Versionchanged
Changed in version 0.12.0: Property is now a `str` instead of `bytes`.
```

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

### DigitalSequence.description

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/seq.md

Gets the description of the sequence.

```APIDOC
## DigitalSequence.description

### Description
The description of the sequence.

### Type
`str`

### Versionchanged
Changed in version 0.12.0: Property is now a `str` instead of `bytes`.
```

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

### DigitalSequence.accession

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/seq.md

Gets the accession of the sequence.

```APIDOC
## DigitalSequence.accession

### Description
The accession of the sequence.

### Type
`str`

### Versionchanged
Changed in version 0.12.0: Property is now a `str` instead of `bytes`.
```

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

### Load NCBI Taxonomy Database with taxopy

Source: https://github.com/althonos/pyhmmer/blob/master/docs/examples/iterative_search.ipynb

Initializes the taxopy database for taxonomic lookups. Set keep_files=False to avoid saving temporary files.

```python
import taxopy
taxdb = taxopy.TaxDb(keep_files=False)
```

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

### DigitalSequence.length

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/seq.md

Gets the length of the sequence.

```APIDOC
## DigitalSequence.L

### Description
The length of the sequence.

### Type
`int`

### Versionadded
Added in version 0.12.1.
```

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

### DigitalSequence.sequence

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/seq.md

Gets the raw sequence letters as a Python string.

```APIDOC
## DigitalSequence.sequence

### Description
The raw sequence letters, as a Python string.

### Type
`str`
```

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

### DigitalSequence.alphabet

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/seq.md

Gets the biological alphabet used to encode this sequence to digits.

```APIDOC
## DigitalSequence.alphabet

### Description
The biological alphabet used to encode this sequence to digits.

### Type
[`Alphabet`](alphabet.md#pyhmmer.easel.Alphabet), *readonly*

### HINT
Use the `sequence` property to access the sequence digits as a memory view, allowing to access the individual bytes. This can be combined with `numpy.asarray` to get the sequence as an array with zero-copy.

### Versionadded
Added in version 0.10.4: `pickle` protocol support.
```

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

### Create and Access MatrixD Elements

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/linalg.md

Demonstrates creating a MatrixD, setting individual elements using indexing, and accessing rows as VectorD objects. Also shows conversion to a NumPy array and performing NumPy operations.

```python
>>> m = MatrixD.zeros(2, 2)
>>> m[0, 0] = 3.0
>>> m
MatrixD([[3.0, 0.0], [0.0, 0.0]])
```

```python
>>> m = MatrixD([ [1.0, 2.0], [3.0, 4.0] ])
>>> m[0]
VectorD([1.0, 2.0])
```

```python
>>> m = MatrixD([ [1.0, 2.0], [3.0, 4.0] ])
>>> numpy.asarray(m)
array([[1., 2.],
       [3., 4.]])
```

```python
>>> m = MatrixD([ [1.0, 2.0], [3.0, 4.0] ])
>>> numpy.log2(m)
array([[0.       , 1.       ],
       [1.5849625, 2.       ]])
```

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

### rewind()

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/parsers.md

Rewinds the file back to the beginning, allowing profiles to be read again from the start.

```APIDOC
## rewind()

### Description
Rewinds the file back to the beginning, allowing profiles to be read again from the start.
```

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

### Download PKSI-AT HMM profile

Source: https://github.com/althonos/pyhmmer/blob/master/docs/examples/active_site.ipynb

Download the PKSI-AT HMM file from the AntiSMASH GitHub repository using urllib.request and save it locally. This requires shutil for file copying.

```python
import shutil
from urllib.request import urlopen

with urlopen('https://raw.githubusercontent.com/antismash/antismash/refs/heads/8-0-stable/antismash/modules/active_site_finder/data/PKSI-AT.hmm2') as src:
    with open("PKSI-AT.hmm2", "wb") as dst:
        shutil.copyfileobj(src, dst)
```

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

### DigitalSequence.residue_markups

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/seq.md

Gets extra residue markups, mapping information to each position. Keys and values are not decoded.

```APIDOC
## DigitalSequence.residue_markups

### Description
Extra residue markups, mapping information to each position. Keys and values are not decoded, since they are not necessarily valid UTF-8 bytestrings.

### Type
`dict`

### Versionadded
Added in version 0.4.6.
```

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

### Traces.__init__

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/traces.md

Creates a new Traces block, which is a collection of Trace objects.

```APIDOC
## __init__()

### Description
Create a new trace block from an iterable of [`Trace`](#pyhmmer.plan7.Trace) objects.
```

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

### Using HMMPressedFile with a context manager

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/parsers.md

Shows how to open and read an optimized profile from a pressed HMM database file using HMMPressedFile within a 'with' statement for automatic closing.

```python
>>> with HMMPressedFile("tests/data/hmms/db/Thioesterase.hmm") as hmm_db:
...     optimized_profile = hmm_db.read()
```

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

### Accessing TopHits Information

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/plan7/results.md

Shows how to get the number of top hits using len() and access individual hits by index.

```default
>>> len(hits)
1
>>> hits[0].name
'938293.PRJEB85.HG003687_113'
```

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

### Extract HMM from Iterations

Source: https://github.com/althonos/pyhmmer/blob/master/docs/examples/iterative_search.ipynb

Extracts the HMM object from the last iteration of a search. This HMM can then be modified, for example, to set cutoffs.

```python
hmm = iterations[-1].hmm
```

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

### Get HMM Consensus Sequence

Source: https://github.com/althonos/pyhmmer/blob/master/docs/examples/msa_to_hmm.ipynb

Retrieves the consensus sequence of the built HMM. This provides a summary of the conserved residues across the alignment.

```python
hmm.consensus
```

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

### View pyhmmer.plan7 documentation

Source: https://github.com/althonos/pyhmmer/blob/master/README.md

Access the pyhmmer.plan7 module documentation directly from the command line using pydoc. This provides an API reference for plan7 objects, including results.

```console
pydoc pyhmmer.plan7
```

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

### Compare HMM File Loading Times

Source: https://github.com/althonos/pyhmmer/blob/master/docs/examples/performance_tips.ipynb

Demonstrates the performance difference between loading HMMs from text (.hmm) and binary (.h3m) files. Binary files are significantly faster to load.

```python
import pyhmmer
%timeit list(pyhmmer.plan7.HMMFile("data/hmms/txt/RREFam.hmm"))
%timeit list(pyhmmer.plan7.HMMFile("data/hmms/bin/RREFam.h3m"))
```

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

### AlphabetMismatch Example

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/errors/value.md

This error is raised when arguments to a function have mismatching alphabets, such as passing a DigitalSequence with a DNA alphabet to a Builder expecting an amino alphabet.

```python
>>> seq = easel.DigitalSequence(easel.Alphabet.dna())
>>> builder = plan7.Builder(easel.Alphabet.amino())
>>> builder.build(seq, plan7.Background(seq.alphabet))
Traceback (most recent call last):
  ...
pyhmmer.errors.AlphabetMismatch: Expected amino alphabet, found DNA alphabet
```

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

### Plot Score Differences

Source: https://github.com/althonos/pyhmmer/blob/master/docs/examples/iterative_search.ipynb

Plots the calculated score differences to visualize the distribution and aid in identifying optimal cutoff points. Requires matplotlib to be installed.

```python
import matplotlib.pyplot as plt

plt.plot(diff)
plt.ylabel("dscore")
plt.xlabel("Hit rank")
plt.show()
```

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

### VectorU8 Initialization and Operations

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/easel/linalg.md

Methods for creating and operating on VectorU8, which stores byte-sized unsigned integers.

```APIDOC
## VectorU8

### __init__(iterable=())

Create a new byte vector from the given data.

### argmax()

Return index of the maximum element in the vector.

* **Raises:**
  **ValueError** – When called on an empty vector.

### argmin()

Return index of the minimum element in the vector.

* **Raises:**
  **ValueError** – When called on an empty vector.

### copy()

Create a copy of the vector, allocating a new buffer.

### max()

Return value of the maximum element in the vector.

* **Raises:**
  **ValueError** – When called on an empty vector.

### min()

Return value of the minimum element in the vector.

* **Raises:**
  **ValueError** – When called on an empty vector.

### reverse()

Reverse the vector, in place.

### sum()

Returns the scalar sum of all elements in the vector.
```

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

### Connect to HMMER Daemon Client

Source: https://github.com/althonos/pyhmmer/blob/master/docs/api/daemon/client.md

Instantiate and connect a client to the HMMER daemon server. The client can also be used as a context manager.

```python
>>> client = daemon.Client("127.0.0.1", 51371)
>>> client.connect()
```

```python
>>> with daemon.Client() as client:
...    client.search_hmm(thioesterase)
<pyhmmer.plan7.TopHits object at 0x...>
```