diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6cb3d906..7e35eefd 100755 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -30,6 +30,7 @@ repos: rev: 1.16.0 hooks: - id: blacken-docs + exclude: docs/tutorial.md - repo: https://github.com/crate-ci/typos rev: typos-dict-v0.11.2 diff --git a/README.md b/README.md index 8f2f7cff..2ed247b5 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,8 @@ _An Efficient and Ergonomic Python Binding Library for BLAT_ [![c](https://img.shields.io/badge/C-A8B9CC.svg?style=for-the-badge&logo=C&logoColor=black)](https://www.gnu.org/software/gnu-c-manual/) [![pypi](https://img.shields.io/pypi/v/pxblat.svg?style=for-the-badge)][pypi] [![conda](https://img.shields.io/conda/vn/bioconda/pxblat?style=for-the-badge)][conda] -![platform](https://img.shields.io/static/v1?style=for-the-badge&label=platform&message=macos%20%7C%20linux&color=brightgreen) +![Linux](https://img.shields.io/badge/-Linux-grey?logo=linux&style=for-the-badge) +![macOS](https://img.shields.io/badge/-OSX-black?logo=apple&style=for-the-badge) [![pyversion](https://img.shields.io/pypi/pyversions/pxblat?style=for-the-badge)][pypi] [![tests](https://img.shields.io/github/actions/workflow/status/cauliyang/pxblat/tests.yml?style=for-the-badge&logo=github&label=Tests)](https://github.com/cauliyang/pxblat/actions/workflows/tests.yml) [![Codecov](https://img.shields.io/codecov/c/github/cauliyang/pxblat/main?style=for-the-badge)](https://app.codecov.io/gh/cauliyang/pxblat) diff --git a/docs/_templates/base.html b/docs/_templates/base.html index 5884beaf..8a40e363 100644 --- a/docs/_templates/base.html +++ b/docs/_templates/base.html @@ -1,6 +1,5 @@ {% extends "!base.html" %} {% block announce %}

- Now Please Cite Me v0.3.10

diff --git a/docs/conf.py b/docs/conf.py index d16a780e..6af9b600 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -82,6 +82,7 @@ # so a file named 'default.css' will overwrite the builtin 'default.css'. html_static_path = ["_static"] + myst_heading_anchors = 3 myst_enable_extensions = [ "dollarmath", diff --git a/docs/installation.md b/docs/installation.md index 02a0116e..ee814a27 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -1,95 +1,74 @@ -# Install +# **Installation Guide** -## **Prerequisites** +Welcome to the installation guide for **PxBLAT**! +Below, you'll find straightforward instructions on how to install **PxBLAT** on your system. +You can choose between `CONDA` and `PyPI` for installation, depending on your preference. -```{tip} -I highly recommend to install `PxBLAT` via `CONDA` such that you do not need to -install dependencies [goto ➡️](#get-started). -``` +## Get started -Before you begin with the installation and use of **PxBLAT**, there are certain prerequisites that need to be met. -The following sections detail the necessary software, hardware, and knowledge prerequisites that you should have before you start. -**PxBLAT** has been tested and runs on the following operating systems **Linux** and **MacOS**. -Choosing appropriate dependencies manager according to the operating systems. -You should have an active and stable internet connection for downloading and installing the software: +Installing **PxBLAT** is a breeze, whether you prefer using `CONDA` or `PyPI`. +Simply follow the tabs below to choose your preferred installation method. `````{md-tab-set} -````{md-tab-item} Brew +````{md-tab-item} Pip + +To install using `pip`, run the following command in your terminal: + ```{code-block} bash -brew install htslib openssl +pip install pxblat ``` + +This will fetch the latest version of **PxBLAT** and install it on your system. ```` ````{md-tab-item} Conda + +To install using `conda`, execute the following command: + ```{code-block} bash -conda install htslib openssl -``` -```` -````{md-tab-item} Apt-get -```{code-block} bash -apt-get update && apt-get install libhts-dev libssl-dev +conda install pxblat ``` +This command will install **PxBLAT** from the [conda] repository. ```` ````` -## **Get Started** +## Compatibility and Support -Installing **PxBLAT** via `CONDA` **do not requires** the prerequisites. -Installing **PxBLAT** via `PyPI` requires the prerequisites. -Once you have confirmed the prerequisites, you can proceed with the software installation: +Below is a compatibility matrix that shows the support status of **PxBLAT** across different platforms and Python versions. -`````{md-tab-set} +### [Conda Support][conda] -````{md-tab-item} Conda -```{code-block} bash -conda install pxblat -``` -```` - -````{md-tab-item} Pip -```{code-block} bash -pip install pxblat -``` -```` - -````` +| Python Version | Linux x86_64 | macOS Intel | +| :------------: | :----------: | :---------: | +| 3.9 | ✅ | ✅ | +| 3.10 | ✅ | ✅ | +| 3.11 | ✅ | ✅ | +| 3.12 | ⚫ | ⚫ | -``````{warning} -You meet the issue _*.h cannot found_ or _undefined symbol **_ If you install `pxblat` by `pip`. -If you have installed the prerequisites, the problem is caused by incorrect environment variable {envvar}`CFLAGS`, `CXXFLAGS`, -and `LDFLAGS`, which direct compiler and linker find right location of -dependencies so as to compile and link code properly. -**The easy solution** is to install **PxBLAT** via `conda`. -You can also set proper environment variable if `conda` is not accessible. +### [PyPI Support][pypi] +| Python Version | Linux x86_64 | macOS Intel | macOS Apple Silicon | +| :------------: | :----------: | :---------: | :-----------------: | +| 3.9 | ✅ | ✅ | ✅ | +| 3.10 | ✅ | ✅ | ✅ | +| 3.11 | ✅ | ✅ | ✅ | +| 3.12 | ⚫ | ⚫ | ⚫ | -`````{md-tab-set} +## Frequently Asked Questions (FAQ) -````{md-tab-item} Bash/Zsh -```{code-block} bash -export CFLAGS="-Idependencies" -export CXXFLAGS="-Idependencies" -... -``` -```` +- **Q1**: I'm unable to install `PxBLAT` via `Conda` on my macOS device with an Arm-based processor (M1 or M2). What should I do? -````{md-tab-item} Fish -```{code-block} fish -set -x CFLAGS="-Idependencies" -set -x CXXLAGS="-Idependencies" -... -``` -```` -````` + > **A**: Currently, `Conda` provides **PxBLAT** built for x86 architectures. For Arm-based macOS devices, we recommend installing **PxBLAT** via `PyPI` instead: -`````` + ```bash + pip install pxblat + ``` -## **FAQ (Frequently Asked Questions)** +You've successfully installed **PxBLAT**! Feel free to dive into a real usage case ({doc}`tutorial`) to start exploring its functionalities. -1. I cannot download `PxBLAT` via `Conda` in MacOS with Arm (M1 or M2). + -A: So far, conda build `PxBLAT` in x86 instead of arrch64. -Hence we can install [prerequisites](#prerequisites) manually via `brew` or `Conda`. -Then, we can use `pip install pxblat` to install `PxBLAT`. +[conda]: https://anaconda.org/bioconda/pxblat +[pypi]: https://pypi.org/project/pxblat/ diff --git a/docs/tutorial.md b/docs/tutorial.md index 7a920985..bbcb0e3b 100644 --- a/docs/tutorial.md +++ b/docs/tutorial.md @@ -1,82 +1,171 @@ # **Tutorial** -`PxBLAT` binds the codebase of [BLAT(v.37x1)][BLAT(v.37x1)], and aims to provide efficient and -ergonomic APIs. Let's take the journey to show features `PxBLAT` provides. +```{warning} +Make sure you have installed PxBLAT, otherwise please go-to ({doc}`installation`). +``` -## APIs Compared to `BLAT` +```{important} +We do not assume you already know common formats and BLAT, which is a standout within the bioinformatics landscape and is recognized for its capability to conduct genome sequence alignments. +BLAT can help us know where one or several sequences can be mapped to the reference for nucleotide or peptide sequences. +Assume we have multiple sequences, and want to know where these sequences can be mapped in reference sequence. +After reading the tutorial, you are supported to know how to use PxBLAT to align your sequences. +``` -So far, `PxBLAT` provides four main APIs, including {class}`.Client`, {class}`.Server`, {func}`.two_bit_to_fa` and {func}`.fa_to_two_bit`, -as well as other useful functions ({doc}`reference`). -`PxBLAT` is able to finish the most significant features of `BLAT`. -Here is a table in which the features are compared. +**PxBLAT** binds the codebase of [BLAT(v.37x1)][BLAT(v.37x1)], and aims to provide efficient and +ergonomic APIs. Let's take the journey to show features **PxBLAT** provides. -| PxBLAT | BLAT | -| :--------------------- | :----------------------- | -| {class}`.Client` | [gfClient][gfClient] | -| {class}`.Server` | [gfServer][gfServer] | -| {func}`.two_bit_to_fa` | [twoBitToFa][twoBitToFa] | -| {func}`.fa_to_two_bit` | [faToTwoBit][faToTwoBit] | +## 1. Understanding the FASTA Format -## Options Design +In bioinformatics, the FASTA format is a widely used text-based format for representing nucleotide sequences or peptide sequences and their associated information. +Below, we will introduce the FASTA format, its structure, and how it is utilized in bioinformatics applications. -`PxBLAT` uses a extra class to hold and change parameters for {class}`.Server` -and {class}`.TwoBitToFaOption`. -The design is a trick to mimic named parameter, and is used in Cpp and Rust. -Python may not need to the design but it still benefit if the parameters are too -long. -For example, `PxBLAT` can create and change parameters of {class}`.Server` via {meth}`.Server.create_option`. -The chain methods of options is builder pattern which is used in Cpp and Rust. +The FASTA format is a simple, text-based format for representing biological sequences. +Each entry in a FASTA file begins with a single-line description, followed by the sequence data. +The description line is distinguished from the sequence data by a greater-than (`>`) symbol at the beginning. -```{tip} -Click the blinking circle cross, and you will be blessed and get more information. +### Structure of a FASTA File + +Here is an example to illustrate the structure of a FASTA file: + +``` +>sequence1 +ATGCTAGCTAGCTAGCTAGCTAGCTA +GCTAGCTAGCTAGCTAGCTAGCTAGC +TAGCTAGCTAGCTAGCTAGCTAGCTA ``` -```{eval-rst} -.. code-block:: python - :linenos: +In this example: - from pxblat import Server +- `>sequence1` are description lines for two different sequences. +- The sequences themselves are represented in the lines following the description lines. +- Sequences can span multiple lines for readability, and there are no line length restrictions. - server_option = Server.create_option().withStepSize(3).withTileSize(10).build() # (1)! - server = Server("localhost", port, two_bit, server_option) +In bioinformatics, the FASTA format is used to represent sequences for various applications, such as: -.. code-annotations:: - #. we change step size and tile size +- Sequence alignment: Comparing sequences to find similarities and differences. +- Database search: Searching for sequences in large databases. +- Phylogenetics: Studying the evolutionary relationships between sequences. + +The FASTA format is a fundamental part of bioinformatics, providing a simple and efficient way to represent biological sequences. +Understanding this format is crucial for anyone looking to work in the field or use bioinformatics tools, including **PxBLAT**. + +## 2. Prepare Example Data + +### Download sequences and reference examples + +- Let's create a new directory first. + +```bash +mkdir tutorial +cd tutorial +``` + +- Download reference data {download}`⬇️ test_ref.fa `, which is fasta format. + +````{example} Download via wget +:collapsible: close + +```bash +wget https://raw.githubusercontent.com/ylab-hi/pxblat/main/tests/data/test_ref.fa +``` + +```` + +Let's check the reference data + +```console +$ head test_ref.fa +>chr1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +taaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccta +accctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaac +cctaacccaaccctaaccctaaccctaaccctaaccctaaccctaacccc +taaccctaaccctaaccctaaccctaacctaaccctaaccctaaccctaa +ccctaaccctaaccctaaccctaaccctaacccctaaccctaaccctaaa +ccctaaaccctaaccctaaccctaaccctaaccctaaccccaaccccaac +cccaaccccaaccccaaccccaaccctaacccctaaccctaaccctaacc +ctaccctaaccctaaccctaaccctaaccctaaccctaacccctaacccc + +$ wc -l test_ref.fa +301 test_ref.fa ``` -The options have same parameter as its command line version of `BLAT`. -{doc}`reference` includes all possible parameters the option will accept. +- Download test sequences {download}`⬇️ test_case1.fa `, which is fasta format. + +````{example} Download via wget +:collapsible: close -## From FASTA to 2bit +```bash +wget https://raw.githubusercontent.com/ylab-hi/pxblat/main/tests/data/test_case1.fa +``` +```` + +Let's check test reference + +```bash +$ head test_case1.fa +>case1 +TGAGAGGCATCTGGCCCTCCCTGCGCTGTGCCAGCAGCTTGGAGAACCCA +CACTCAATGAACGCAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTC +TCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCA +A +``` + +Now we already have `test_case1.fa` and `test_ref.fa` for following analysis. + +```bash +$ ls +test_case1.fa test_ref.fa +``` -Before we query certain sequence to a reference, we need to generate [.2bit][.2bit] file from [fasta][fasta] format. -`PxBLAT` provides a free function {func}`.fa_to_two_bit`. -Also, `PxBLAT` support to convert the `.2bit` file back to fasta format via {func}`.two_bit_to_fa`, for example, +## 3. Convert FASTA to 2bit + +Before we query certain sequence to a reference `test_ref.fa`, we need to convert [fasta][fasta] format to [.2bit][.2bit] file for reference sequence `test_ref.fa`. +**PxBLAT** provides a function {func}`.fa_to_two_bit`. +Also, **PxBLAT** supports to convert the `.2bit` file back to fasta format via {func}`.two_bit_to_fa`, for example, ```{tip} -The source code includes [chr20.fa] and [chr20.2bit] as well, making it easy for users to give it a try. +Click the blinking circle cross, and you will be blessed and get more information. ``` ```{eval-rst} .. code-block:: python + :name: fa_to_two_bit_block :linenos: from pxblat import fa_to_two_bit fa_to_two_bit( - ["fasta1.fa"], # (1)! - "out.2bit", # (2)! + ["test_ref.fa"], # (1)! + "test_ref.2bit", # (2)! noMask=False, stripVersion=False, ignoreDups=False, useLong=False, ) + print("Done") + .. code-annotations:: #. Same as `BLAT`, :func:`.fa_to_two_bit` can accept multilple inputs #. Output file path ``` +Let's create a Python file named `2bit.py`, and copy and paste [code above](#fa_to_two_bit_block) to `2bit.py`. +Then, execute the `2bit.py` + +```bash +python 2bit.py +``` + +After, we will get a new file named `test_ref.2bit`, which is the 2bit file we +need to align sequences to reference. + +```bash +$ ls +2bit.py test_case1.fa test_ref.2bit test_ref.fa +``` + The code equals `faToTwoBit fasta1.fa out.2bit` by `BLAT(v. 37x1)`. ```bash @@ -91,282 +180,379 @@ options: -stripVersion Strip off version number after '.' for GenBank accessions. -ignoreDups Convert first sequence only if there are duplicate sequence names. Use 'twoBitDup' to find duplicate sequences. -$ faToTwoBit fasta1.fa out.2bit +$ faToTwoBit test_ref.fa test_ref.2bit $ ls -out.2bit fasta1.fa +test_ref.2bit test_ref.fa ``` -Moreover, `PxBLAT` provides flexible options to allow conducting the conversion in {doc}`cli`. +Moreover, **PxBLAT** provides flexible options to allow conducting the conversion in {doc}`cli`. -## Query Sequences +## 4. Query Sequences -Most simple method to query sequence is to open {class}`pxblat.Server` in context mode +**PxBLAT** contains {class}`pxblat.Server` and {class}`pxblat.Client`. +We use them to align our sequences in two steps. + +1. Start {class}`pxblat.Server` +2. {class}`pxblat.Client` send our sequence to {class}`pxblat.Server` for + alignment + +Generally, {class}`pxblat.Server` has three status including `preparing`, `ready`, and `stop`. +It only accepts sequence alignment task in `ready` status. +Hence, in real life we need to make sure the {class}`pxblat.Server` is in `ready` status before {class}`pxblat.Client`send sequences. +**PxBLAT** allow this process more smooth without bothering intermediate file. + +**PxBLAT** provide several ways to start the {class}`pxblat.Server`. + +### 4.1 Start {class}`pxblat.Server` in context mode ```{eval-rst} .. code-block:: python + :name: query_context_block :linenos: - from pxblat import Server, Client + from pxblat import Client, Server - client = Client( - host="localhost", - port=65000, # (1)! - seq_dir=two_bit, # (2)! - min_score=20, - min_identity=90, - ) - server_option = Server.create_option().withCanStop(True).withStepSize(5).build() # (3)! - with Server("localhost", port, two_bit, server_option) as server: - work() # (4)! - server.wait_for_ready() # (5)! - result1 = client.query("ATCG") # (6)! - result2 = client.query("AtcG") # (7)! - result3 = client.query(["ATCG", "ATCG"]) # (8)! - result4 = client.query(["fasta1.fa", "fasta2.fa"]) # (9)! - result5 = client.query(["cgTA", "fasta.fa"]) # (10)! + def query_context(): + host = "localhost" # (1)! + port = 65000 # (2)! + seq_dir = "." # (3)! + two_bit = "./test_ref.2bit" # (4)! + + client = Client( + host=host, + port=port, + seq_dir=seq_dir, + min_score=20, # (5)! + min_identity=90, # (6)! + ) + + with Server(host, port, two_bit, can_stop=True, step_size=5) as server: + # work() assume work() is your own function that takes time to prepare something + server.wait_ready() # (7)! + result1 = client.query("ATCG") # (8)! + result2 = client.query("AtcG") # (9)! + result3 = client.query("test_case1.fa") # (10)! + result4 = client.query(["ATCG", "ATCG"]) # (11)! + result5 = client.query(["test_case1.fa"]) # (12)! + result6 = client.query(["cgTA", "test_case1.fa"]) # (13)! + print(result3[0]) # print result + + + if __name__ == "__main__": + query_context() .. code-annotations:: - #. The port number of current running :class:`.Server` - #. The two bit files from reference, and we can get it via :func:`.fa_to_two_bit` or via :doc:`cli` - #. Create :class:`.ServerOption` with specific parameters for :class:`.Server` - #. We can do some other stuffs that consuming time - #. Block current thread to wait server to be ready - #. :meth:`.Client.query` accepts a :class:`str` consisting of DNA or Protein Sequences, e.g. `"ATCG"` - #. :meth:`.Client.query` accepts a path of Fasta file, e.g. `"data/fasta1.fa"` - #. :meth:`.Client.query` accepts a :class:`list` of :class:`str` consisting of DNA or Protein Sequences, e.g. `["ATCG","CTGAG"]` - #. :meth:`.Client.query` accepts a :class:`list` of path of Fasta files, e.g. `["data/fasta1.fa", "data/fasta2.fa"]` - #. :meth:`.Client.query` accepts a :class:`list` of :class:`str` and path, e.g. `["ATCG", "data/fasta1.fa"]` + #. :attr:`.Client.host` is the hostname or IP address of the current running :class:`.Server`. + #. :attr:`.Client.post` is the port number of the current running :class:`.Server`. + #. :attr:`.Client.seq_dir` is the directory including `test_ref.fa` and `test_ref.2bit` + #. `two_bit` is the 2bit file that :ref:`we already create ` + #. :attr:`.Client.min_score` is the minimum score for the alignment. + #. :attr:`.Client.min_identity` is the minimum identity for the alignment. + #. block current thread to wait server to be ready + #. :meth:`.Client.query` accepts a :class:`str` consisting of nucleotide or peptide sequences, e.g. `"ATCG"` + #. :meth:`.Client.query` accepts nucleotide or peptide sequences that are case-insensitive, e.g. `"AtcG"` + #. :meth:`.Client.query` accepts a path of fasta file, e.g. `"./test_case1.fa"` + #. :meth:`.Client.query` accepts a :class:`list` of :class:`str` consisting of nucleotide or peptide sequences, e.g. `["ATCG","CTGAG"]` + #. :meth:`.Client.query` accepts a :class:`list` of path of fasta files, e.g. `["test_case1.fa"]` + #. :meth:`.Client.query` accepts a :class:`list` of :class:`str` and path, e.g. `["ATCG", "test_case1.fa"]` ``` {meth}`.Client.query` accepts parameters of several types: -1. Path of Fasta file e.g. `data/fasta1.fa` -2. {class}`list` of {class}`str` consisting of DNA or Protein Sequences, e.g. `["ATCG","CTGAG"]` -3. {class}`list` of path of Fasta files, e.g. `["data/fasta1.fa", "data/fasta2.fa"]` -4. {class}`list` of `str` and path, e.g. `["ATCG", "data/fasta1.fa"]` -5. {meth}`.Client.query` accepts a {class}`list` of {class}`str` and path, e.g. `["ATCG", "data/fasta1.fa"]` +- Path of fasta file e.g. `./test_case1.fa` +- {class}`str` consisting of nucleotide or peptide sequences that are case-insensitive, e.g. `ATCG`, or `ATcg` +- {class}`list` of {class}`str` consisting of nucleotide or peptide sequences that are case-insensitive, e.g. `["AtcG","CTGAG"]` +- {class}`list` of path of fasta files, e.g. `["data/fasta1.fa", "./test_case1.fa"]` +- {class}`list` of `str` and path, e.g. `["ATCG", "data/fasta1.fa"]` -{meth}`.Client.query` return [Bio.SearchIO.QueryResult](#query-result). +Let's Create a new Python script named `query_context.py`, and copy and paste [code above](#query_context_block) to the script. +Then execute the Python script. + +```bash +$ python query_context.py +Program: blat (v.37x1) + Query: case1 (151) + + Target: + Hits: ---- ----- ---------------------------------------------------------- + # # HSP ID + description + ---- ----- ---------------------------------------------------------- + 0 1 chr1 +``` -We may need to query sequences in more general way, for example, +{meth}`.Client.query` return [`QueryResult`](#query-result), which is introduced later. + +### 4.2 Start {class}`pxblat.Server` in general mode ```{eval-rst} .. code-block:: python + :name: query_general_block :linenos: - from pxblat import Server, Client + from pxblat import Client, Server - client = Client( - host="localhost", - port=port, - seq_dir=two_bit, - min_score=20, - min_identity=90, - wait_ready=True, # (1)! - ) + def query_general(): + host = "localhost" + port = 65000 + seq_dir = "." + two_bit = "./test_ref.2bit" + + client = Client( + host=host, + port=port, + seq_dir=seq_dir, + min_score=20, + min_identity=90, + ) + + server = Server(host, port, two_bit, can_stop=True, step_size=5) + server.start() # (1)! + # work() assume work() is your own function that takes time to prepare something + server.wait_ready() # (2)! + result1 = client.query(["actg", "test_case1.fa"]) + # another_work() assume the func is your own function that takes time + result2 = client.query("test_case1.fa") + server.stop() # (3)! + + print(f"{result1=}") + print(f"{result2=}") - server_option = Server.create_option().withCanStop(True).withStepSize(5).build() - server = Server("localhost", port, two_bit, server_option) - server.start() - work() # (2)! - # server.wait_ready() - # (3)! - result1 = client.query(["actg", "fasta.fa"]) - other_work() - result2 = client.query("fasta.fa") - server.stop() # (4)! + + if __name__ == "__main__": + query_general() .. code-annotations:: - #. The parameter `wait_ready` is used to control if the client need to check and wait current server to be ready or query directly. - #. May a task consuming long time - #. No need to wait current running server to be ready, and the job will be done by :class:`.Client` - #. Stop the current running server + #. start server + #. block until the server is ready + #. stop the current running server +``` + +```{note} +the explanation of parameters including `two_bit` and `seq_dir` etc. is same as +[previous code](#query_context_block) ``` -Although {class}`.Server` and {class}`.Client` already consider most contexts, `PxBLAT` provides {class}`.ClientThread` that can launch a thread to +Let's Create a new Python script named `query_general.py`, and copy and paste [code above](#query_general_block) to the script. +Then execute the Python script. + +```bash +$ python query_general.py +result1=[None, QueryResult(id='case1', 1 hits)] +result2=[QueryResult(id='case1', 1 hits)] +``` + +```{note} +`None` means the sequence cannot be mapped to the reference. +``` + +Although {class}`.Server` and {class}`.Client` already consider most contexts, **PxBLAT** provides {class}`.ClientThread` that can launch a thread to query sequence. -However, {class}`.ClientThread` only query one sequence at one time. -Its APIs are still not stable so far. Free feel to check that if you have interests. -## Query Result +## 5. Query Result + +Right now we know how to query certain sequence to the reference, and let's dive into the query result and manipulate that together. + +Here we use contexts mode to align sequence, and modify a little bit based on [previous code](#query_context_block) + +````{example} query_context (hint: convenient to copy) +:collapsible: close -`PxBLAT` aims to introduce as few concepts as possible so that users do not need to take time to learn. -The query result is the same as `QueryResult` of [Bio][Bio]. -Hence, we can manipulate the query result as shown below. +```python +from pxblat import Client, Server + +def query_context(): + host = "localhost" + port = 65000 + seq_dir = "." + two_bit = "./test_ref.2bit" + client = Client( + host=host, + port=port, + seq_dir=seq_dir, + min_score=20, + min_identity=90, + ) + with Server(host, port, two_bit, can_stop=True, step_size=5) as server: + # work() assume work() is your own function that takes time to prepare something + server.wait_ready() + result1 = client.query("ATCG") + result2 = client.query("AtcG") + result3 = client.query("test_case1.fa") + result4 = client.query(["ATCG", "ATCG"]) + result5 = client.query(["test_case1.fa"]) + result6 = client.query(["cgTA", "test_case1.fa"]) + return [result1, result2, result3, result4, result5, result6] +``` +```` ```{eval-rst} -.. py:class:: QueryResult - - Class representing search results from a single query. - - QueryResult is the container object that stores all search hits from a - single search query. It is the top-level object returned by SearchIO's two - main functions, ``read`` and ``parse``. Depending on the search results and - search output format, a QueryResult object will contain zero or more Hit - objects (see Hit). - - You can take a quick look at a QueryResult's contents and attributes by - invoking ``print`` on it:: - - >>> from Bio import SearchIO - >>> qresult = next(SearchIO.parse('Blast/mirna.xml', 'blast-xml')) - >>> print(qresult) - Program: blastn (2.2.27+) - Query: 33211 (61) - mir_1 - Target: refseq_rna - Hits: ---- ----- ---------------------------------------------------------- - # # HSP ID + description - ---- ----- ---------------------------------------------------------- - 0 1 gi|262205317|ref|NR_030195.1| Homo sapiens microRNA 52... - 1 1 gi|301171311|ref|NR_035856.1| Pan troglodytes microRNA... - 2 1 gi|270133242|ref|NR_032573.1| Macaca mulatta microRNA ... - 3 2 gi|301171322|ref|NR_035857.1| Pan troglodytes microRNA... - 4 1 gi|301171267|ref|NR_035851.1| Pan troglodytes microRNA... - 5 2 gi|262205330|ref|NR_030198.1| Homo sapiens microRNA 52... - 6 1 gi|262205302|ref|NR_030191.1| Homo sapiens microRNA 51... - 7 1 gi|301171259|ref|NR_035850.1| Pan troglodytes microRNA... - 8 1 gi|262205451|ref|NR_030222.1| Homo sapiens microRNA 51... - 9 2 gi|301171447|ref|NR_035871.1| Pan troglodytes microRNA... - 10 1 gi|301171276|ref|NR_035852.1| Pan troglodytes microRNA... - 11 1 gi|262205290|ref|NR_030188.1| Homo sapiens microRNA 51... - ... - - If you just want to know how many hits a QueryResult has, you can invoke - ``len`` on it. Alternatively, you can simply type its name in the interpreter:: - - >>> len(qresult) - 100 - >>> qresult - QueryResult(id='33211', 100 hits) - - QueryResult behaves like a hybrid of Python's built-in list and dictionary. - You can retrieve its items (Hit objects) using the integer index of the - item, just like regular Python lists:: - - >>> first_hit = qresult[0] - >>> first_hit - Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps) - - You can slice QueryResult objects as well. Slicing will return a new - QueryResult object containing only the sliced hits:: - - >>> sliced_qresult = qresult[:3] # slice the first three hits - >>> len(qresult) - 100 - >>> len(sliced_qresult) - 3 - >>> print(sliced_qresult) - Program: blastn (2.2.27+) - Query: 33211 (61) - mir_1 - Target: refseq_rna - Hits: ---- ----- ---------------------------------------------------------- - # # HSP ID + description - ---- ----- ---------------------------------------------------------- - 0 1 gi|262205317|ref|NR_030195.1| Homo sapiens microRNA 52... - 1 1 gi|301171311|ref|NR_035856.1| Pan troglodytes microRNA... - 2 1 gi|270133242|ref|NR_032573.1| Macaca mulatta microRNA ... - - Like Python dictionaries, you can also retrieve hits using the hit's ID. - This is useful for retrieving hits that you know should exist in a given - search:: - - >>> hit = qresult['gi|262205317|ref|NR_030195.1|'] - >>> hit - Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps) - - You can also replace a Hit in QueryResult with another Hit using either the - integer index or hit key string. Note that the replacing object must be a - Hit that has the same ``query_id`` property as the QueryResult object. - - If you're not sure whether a QueryResult contains a particular hit, you can - use the hit ID to check for membership first:: - - >>> 'gi|262205317|ref|NR_030195.1|' in qresult - True - >>> 'gi|262380031|ref|NR_023426.1|' in qresult - False - - Or, if you just want to know the rank / position of a given hit, you can - use the hit ID as an argument for the ``index`` method. Note that the values - returned will be zero-based. So zero (0) means the hit is the first in the - QueryResult, three (3) means the hit is the fourth item, and so on. If the - hit does not exist in the QueryResult, a ``ValueError`` will be raised. - - >>> qresult.index('gi|262205317|ref|NR_030195.1|') - 0 - >>> qresult.index('gi|262205330|ref|NR_030198.1|') - 5 - >>> qresult.index('gi|262380031|ref|NR_023426.1|') - Traceback (most recent call last): - ... - ValueError: ... - - To ease working with a large number of hits, QueryResult has several - ``filter`` and ``map`` methods, analogous to Python's built-in functions with - the same names. There are ``filter`` and ``map`` methods available for - operations over both Hit objects or HSP objects. As an example, here we are - using the ``hit_map`` method to rename all hit IDs within a QueryResult:: - - >>> def renamer(hit): - ... hit.id = hit.id.split('|')[3] - ... return hit - >>> mapped_qresult = qresult.hit_map(renamer) - >>> print(mapped_qresult) - Program: blastn (2.2.27+) - Query: 33211 (61) - mir_1 - Target: refseq_rna - Hits: ---- ----- ---------------------------------------------------------- - # # HSP ID + description - ---- ----- ---------------------------------------------------------- - 0 1 NR_030195.1 Homo sapiens microRNA 520b (MIR520B), micr... - 1 1 NR_035856.1 Pan troglodytes microRNA mir-520b (MIR520B... - 2 1 NR_032573.1 Macaca mulatta microRNA mir-519a (MIR519A)... - ... - - The principle for other ``map`` and ``filter`` methods are similar: they accept - a function, applies it, and returns a new QueryResult object. - - There are also other methods useful for working with list-like objects: - ``append``, ``pop``, and ``sort``. More details and examples are available in - their respective documentations. - - Finally, just like Python lists and dictionaries, QueryResult objects are - iterable. Iteration over QueryResults will yield Hit objects:: - - >>> for hit in qresult[:4]: # iterate over the first four items - ... hit - ... - Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps) - Hit(id='gi|301171311|ref|NR_035856.1|', query_id='33211', 1 hsps) - Hit(id='gi|270133242|ref|NR_032573.1|', query_id='33211', 1 hsps) - Hit(id='gi|301171322|ref|NR_035857.1|', query_id='33211', 2 hsps) - - If you need access to all the hits in a QueryResult object, you can get - them in a list using the ``hits`` property. Similarly, access to all hit IDs is - available through the ``hit_keys`` property. - - >>> qresult.hits - [Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps), ...] - >>> qresult.hit_keys - ['gi|262205317|ref|NR_030195.1|', 'gi|301171311|ref|NR_035856.1|', ...] + +.. code-block:: pycon + :name: query_result_block + + >>> from pxblat import Client, Server + >>> def query_context(): + ... host = "localhost" + ... port = 65000 + ... seq_dir = "." + ... two_bit = "./test_ref.2bit" + ... client = Client( + ... host=host, + ... port=port, + ... seq_dir=seq_dir, + ... min_score=20, + ... min_identity=90, + ... ) + ... with Server(host, port, two_bit, can_stop=True, step_size=5) as server: + ... # work() assume work() is your own function that takes time to prepare something + ... server.wait_ready() + ... result1 = client.query("ATCG") + ... result2 = client.query("AtcG") + ... result3 = client.query("test_case1.fa") + ... result4 = client.query(["ATCG", "ATCG"]) + ... result5 = client.query(["test_case1.fa"]) + ... result6 = client.query(["cgTA", "test_case1.fa"]) + ... return [result1, result2, result3, result4, result5, result6] + >>> results = query_context() # get all alignment results + >>> results + [[None], [None], [QueryResult(id='case1', 1 hits)], [None, None], [QueryResult(id='case1', 1 hits)], [None, QueryResult(id='case1', 1 hits)]] + >>> results[2] # let's pick up the result of test_case1.fa + [QueryResult(id='case1', 1 hits)] + >>> result3 = results[2] + >>> result3 + [QueryResult(id='case1', 1 hits)] + >>> print(result3[0]) # let's show information of the result + Program: blat (v.37x1) + Query: case1 (151) + + Target: + Hits: ---- ----- ---------------------------------------------------------- + # # HSP ID + description + ---- ----- ---------------------------------------------------------- + 0 1 chr1 + >>> result = result3[0] # let's get the element in the result list + >>> result + QueryResult(id='case1', 1 hits) + >>> print(result) + Program: blat (v.37x1) + Query: case1 (151) + + Target: + Hits: ---- ----- ---------------------------------------------------------- + # # HSP ID + description + ---- ----- ---------------------------------------------------------- + 0 1 chr1 + >>> result.hsps # check all high-scoring pairs (HSPs) + [HSP(hit_id='chr1', query_id='case1', 1 fragments)] + >>> result[0] # check the top hsp + Hit(id='chr1', query_id='case1', 1 hsps) + >>> print(result[0]) # show more information about top hsp + Query: case1 + + Hit: chr1 (14999) + + HSPs: ---- -------- --------- ------ --------------- --------------------- + # E-value Bit score Span Query range Hit range + ---- -------- --------- ------ --------------- --------------------- + 0 ? ? ? [0:151] [12699:12850] + >>> top_hsp = result.hsps[0] + >>> top_hsp + HSP(hit_id='chr1', query_id='case1', 1 fragments) + >>> print(top_hsp) + Query: case1 + Hit: chr1 + Query range: [0:151] (1) + Hit range: [12699:12850] (1) + Quick stats: evalue ?; bitscore ? + Fragments: 1 (? columns) + >>> top_hsp.query_id # test_case1's id in top_hsp + 'case1' + >>> top_hsp.query_range # test_case1's query_range in top_hsp + (0, 151) + >>> top_hsp.query_span # test_case1's query_span in top_hsp + 151 + >>> top_hsp.query_start # test_case1's query_start in top_hsp + 0 + >>> top_hsp.query_strand # test_case1's query_strand in top_hsp + 1 + >>> top_hsp.hit_id # in top_hsp, test_case1 hit `chr1` of the reference + 'chr1' + >>> top_hsp.hit_range # in top_hsp, test_case1 hit (12699, 12850) of the reference + (12699, 12850) + >>> top_hsp.hit_start + 12699 + >>> top_hsp.hit_strand # in top_hsp, test_case1 hit strand of the reference (1 means positive strand) + 1 + >>> top_hsp. + top_hsp.aln top_hsp.hit_frame top_hsp.ident_pct top_hsp.query_frame_all + top_hsp.aln_all top_hsp.hit_frame_all top_hsp.is_fragmented top_hsp.query_gap_num + top_hsp.aln_annotation top_hsp.hit_gap_num top_hsp.match_num top_hsp.query_gapopen_num + top_hsp.aln_annotation_all top_hsp.hit_gapopen_num top_hsp.match_rep_num top_hsp.query_id + top_hsp.aln_span top_hsp.hit_id top_hsp.mismatch_num top_hsp.query_inter_ranges + top_hsp.fragment top_hsp.hit_inter_ranges top_hsp.molecule_type top_hsp.query_inter_spans + top_hsp.fragments top_hsp.hit_inter_spans top_hsp.n_num top_hsp.query_is_protein + top_hsp.gap_num top_hsp.hit_range top_hsp.output_index top_hsp.query_range + top_hsp.gapopen_num top_hsp.hit_range_all top_hsp.query top_hsp.query_range_all + top_hsp.hit top_hsp.hit_span top_hsp.query_all top_hsp.query_span + top_hsp.hit_all top_hsp.hit_span_all top_hsp.query_description top_hsp.query_span_all + top_hsp.hit_description top_hsp.hit_start top_hsp.query_end top_hsp.query_start + top_hsp.hit_end top_hsp.hit_start_all top_hsp.query_end_all top_hsp.query_start_all + top_hsp.hit_end_all top_hsp.hit_strand top_hsp.query_features top_hsp.query_strand + top_hsp.hit_features top_hsp.hit_strand_all top_hsp.query_features_all top_hsp.query_strand_all + top_hsp.hit_features_all top_hsp.ident_num top_hsp.query_frame top_hsp.score + +``` + +````{example} query_result code +:collapsible: close + +```{literalinclude} tutorial_data/query_result.py +``` + +```` + +We can precisely determine the regions of our sequence that align with specific parts of the reference. +We are able to know strand, start position, and end position for alignment part +both for our sequence and the reference. +The last part of [code example](#query_result_block) shows all methods of a high-scoring pairs (HSP). + +## 6. APIs Compared to `BLAT` + +So far, **PxBLAT** provides APIs, including {class}`.Client`, {class}`.Server`, {func}`.two_bit_to_fa` and {func}`.fa_to_two_bit`, +as well as other useful functions ({doc}`reference`). +**PxBLAT** is able to finish the most significant features of `BLAT`. +Here is a table in which the features are compared. + +```{list-table} APIs Comparison + :header-rows: 1 + :align: center + + * - PxBLAT + - BLAT + * - {class}`.Client` + - [gfClient][gfClient] + * - {class}`.Server` + - [gfServer][gfServer] + * - {func}`.two_bit_to_fa` + - [twoBitToFa][twoBitToFa] + * - {func}`.fa_to_two_bit` + - [faToTwoBit][faToTwoBit] ``` -## Beyond APIs +## 7. Beyond APIs Even though `PxBLAT` is designed as library, it provides command-line tools using its APIs. That could provide more choices for user according to different situations. {doc}`reference` contain more details, and do not hesitate to check. -## Caveats +```{bug} +please feel free to [edit the tutorial](https://github.com/ylab-hi/pxblat/edit/main/docs/tutorial.md) or [open an issue](https://github.com/ylab-hi/pxblat/issues/new/choose), if you find some unclear or wrong statement. -{class}`.ServerOption` hold most important parameters that are passed to {class}`.Server`. +``` diff --git a/docs/tutorial_data/2bit.py b/docs/tutorial_data/2bit.py new file mode 100644 index 00000000..0df0235a --- /dev/null +++ b/docs/tutorial_data/2bit.py @@ -0,0 +1,11 @@ +from pxblat import fa_to_two_bit + +fa_to_two_bit( + ["test_ref.fa"], + "test_ref.2bit", + noMask=False, + stripVersion=False, + ignoreDups=False, + useLong=False, +) +print("Done") diff --git a/docs/tutorial_data/query_context.py b/docs/tutorial_data/query_context.py new file mode 100644 index 00000000..f1cecda7 --- /dev/null +++ b/docs/tutorial_data/query_context.py @@ -0,0 +1,40 @@ +from pxblat import Client, Server + + +def query_context(): + host = "localhost" + port = 65000 + seq_dir = "." + two_bit = "./test_ref.2bit" + + client = Client( + host=host, + port=port, + seq_dir=seq_dir, + min_score=20, + min_identity=90, + ) + + with Server(host, port, two_bit, can_stop=True, step_size=5) as server: + # work() assume work() is your own function that takes time to prepare something + server.wait_ready() + result1 = client.query("ATCG") + result2 = client.query("AtcG") + result3 = client.query("test_case1.fa") + result4 = client.query(["ATCG", "ATCG"]) + result5 = client.query(["test_case1.fa"]) + result6 = client.query(["cgTA", "test_case1.fa"]) + # print results + print(f"{result1=}") + print(f"{result2=}") + print(f"{result3=}") + print(f"{result3[0]=}") + print(f"{result3[0]=!s}") + print(f"{result4=}") + print(f"{result4[0]=}") + print(f"{result5=}") + print(f"{result6=}") + + +if __name__ == "__main__": + query_context() diff --git a/docs/tutorial_data/query_general.py b/docs/tutorial_data/query_general.py new file mode 100644 index 00000000..0a727797 --- /dev/null +++ b/docs/tutorial_data/query_general.py @@ -0,0 +1,32 @@ +from pxblat import Client, Server + + +def query_general(): + host = "localhost" + port = 65000 + seq_dir = "." + two_bit = "./test_ref.2bit" + + client = Client( + host=host, + port=port, + seq_dir=seq_dir, + min_score=20, + min_identity=90, + ) + + server = Server(host, port, two_bit, can_stop=True, step_size=5) + server.start() + # work() assume work() is your own function that takes time to prepare something + server.wait_ready() + result1 = client.query(["actg", "test_case1.fa"]) + # another_work() assume the func is your own function that takes time + result2 = client.query("test_case1.fa") + server.stop() + + print(f"{result1=}") + print(f"{result2=}") + + +if __name__ == "__main__": + query_general() diff --git a/docs/tutorial_data/query_result.py b/docs/tutorial_data/query_result.py new file mode 100644 index 00000000..d4b83f84 --- /dev/null +++ b/docs/tutorial_data/query_result.py @@ -0,0 +1,72 @@ +from pxblat import Client, Server + + +def query_context(): + host = "localhost" + port = 65000 + seq_dir = "." + two_bit = "./test_ref.2bit" + client = Client( + host=host, + port=port, + seq_dir=seq_dir, + min_score=20, + min_identity=90, + ) + with Server(host, port, two_bit, can_stop=True, step_size=5) as server: + # work() assume work() is your own function that takes time to prepare something + server.wait_ready() + result1 = client.query("ATCG") + result2 = client.query("AtcG") + result3 = client.query("test_case1.fa") + result4 = client.query(["ATCG", "ATCG"]) + result5 = client.query(["test_case1.fa"]) + result6 = client.query(["cgTA", "test_case1.fa"]) + return [result1, result2, result3, result4, result5, result6] + + +def query_result(): + results = query_context() # get all alignment results + results[2] # let's pick up the result of test_case1.fa + result3 = results[2] + print(result3) + print(result3[0]) # let's show information of the result + result = result3[0] # let's get the element in the result list + print(result) + print(result) + print(result.hsps) # check all high-scoring pairs (HSPs) + print(result[0]) # check the top hsp + print(result[0]) # show more information about top hsp + top_hsp = result.hsps[0] + print(top_hsp) + print(top_hsp) + print(top_hsp.query_id) # test_case1's id in top_hsp + print(top_hsp.query_range) # test_case1's query_range in top_hsp + print(top_hsp.query_span) # test_case1's query_span in top_hsp + print(top_hsp.query_start) # test_case1's query_start in top_hsp + print(top_hsp.query_strand) # test_case1's query_strand in top_hsp + print(top_hsp.hit_id) # in top_hsp, test_case1 hit `chr1` of the reference + print(top_hsp.hit_range) # in top_hsp, test_case1 hit (12699, 12850) of the reference + print(top_hsp.hit_start) + print(top_hsp.hit_strand) # in top_hsp, test_case1 hit strand of the reference (1 means positive strand) + # >>> top_hsp. + # top_hsp.aln top_hsp.hit_frame top_hsp.ident_pct top_hsp.query_frame_all + # top_hsp.aln_all top_hsp.hit_frame_all top_hsp.is_fragmented top_hsp.query_gap_num + # top_hsp.aln_annotation top_hsp.hit_gap_num top_hsp.match_num top_hsp.query_gapopen_num + # top_hsp.aln_annotation_all top_hsp.hit_gapopen_num top_hsp.match_rep_num top_hsp.query_id + # top_hsp.aln_span top_hsp.hit_id top_hsp.mismatch_num top_hsp.query_inter_ranges + # top_hsp.fragment top_hsp.hit_inter_ranges top_hsp.molecule_type top_hsp.query_inter_spans + # top_hsp.fragments top_hsp.hit_inter_spans top_hsp.n_num top_hsp.query_is_protein + # top_hsp.gap_num top_hsp.hit_range top_hsp.output_index top_hsp.query_range + # top_hsp.gapopen_num top_hsp.hit_range_all top_hsp.query top_hsp.query_range_all + # top_hsp.hit top_hsp.hit_span top_hsp.query_all top_hsp.query_span + # top_hsp.hit_all top_hsp.hit_span_all top_hsp.query_description top_hsp.query_span_all + # top_hsp.hit_description top_hsp.hit_start top_hsp.query_end top_hsp.query_start + # top_hsp.hit_end top_hsp.hit_start_all top_hsp.query_end_all top_hsp.query_start_all + # top_hsp.hit_end_all top_hsp.hit_strand top_hsp.query_features top_hsp.query_strand + # top_hsp.hit_features top_hsp.hit_strand_all top_hsp.query_features_all top_hsp.query_strand_all + # top_hsp.hit_features_all top_hsp.ident_num top_hsp.query_frame top_hsp.score + + +if __name__ == "__main__": + query_result() diff --git a/docs/tutorial_data/test_case1.fa b/docs/tutorial_data/test_case1.fa new file mode 100644 index 00000000..7f77c66c --- /dev/null +++ b/docs/tutorial_data/test_case1.fa @@ -0,0 +1,5 @@ +>case1 +TGAGAGGCATCTGGCCCTCCCTGCGCTGTGCCAGCAGCTTGGAGAACCCA +CACTCAATGAACGCAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTC +TCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCA +A diff --git a/docs/tutorial_data/test_ref.2bit b/docs/tutorial_data/test_ref.2bit new file mode 100644 index 00000000..f819b533 Binary files /dev/null and b/docs/tutorial_data/test_ref.2bit differ diff --git a/docs/tutorial_data/test_ref.fa b/docs/tutorial_data/test_ref.fa new file mode 100644 index 00000000..d221cbac --- /dev/null +++ b/docs/tutorial_data/test_ref.fa @@ -0,0 +1,301 @@ +>chr1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +taaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccta +accctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaac +cctaacccaaccctaaccctaaccctaaccctaaccctaaccctaacccc +taaccctaaccctaaccctaaccctaacctaaccctaaccctaaccctaa +ccctaaccctaaccctaaccctaaccctaacccctaaccctaaccctaaa +ccctaaaccctaaccctaaccctaaccctaaccctaaccccaaccccaac +cccaaccccaaccccaaccccaaccctaacccctaaccctaaccctaacc +ctaccctaaccctaaccctaaccctaaccctaaccctaacccctaacccc +taaccctaaccctaaccctaaccctaaccctaaccctaacccctaaccct +aaccctaaccctaaccctcgcggtaccctcagccggcccgcccgcccggg +tctgacctgaggagaactgtgctccgccttcagagtaccaccgaaatctg +tgcagaggacaacgcagctccgccctcgcggtgctctccgggtctgtgct +gaggagaacgcaactccgccgttgcaaaggcgcgccgcgccggcgcaggc +gcagagaggcgcgccgcgccggcgcaggcgcagagaggcgcgccgcgccg +gcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcagagaggcgcg +ccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcaga +cacatgctagcgcgtcggggtggaggcgtggcgcaggcgcagagaggcgc +gccgcgccggcgcaggcgcagagacacatgctaccgcgtccaggggtgga +ggcgtggcgcaggcgcagagaggcgcaccgcgccggcgcaggcgcagaga +cacatgctagcgcgtccaggggtggaggcgtggcgcaggcgcagagacgc +aagcctacgggcgggggttgggggggcgtgtgttgcaggagcaaagtcgc +acggcgccgggctggggcggggggagggtggcgccgtgcacgcgcagaaa +ctcacgtcacggtggcgcggcgcagagacgggtagaacctcagtaatccg +aaaagccgggatcgaccgccccttgcttgcagccgggcactacaggaccc +gcttgctcacggtgctgtgccagggcgccccctgctggcgactagggcaa +ctgcagggctctcttgcttagagtggtggccagcgccccctgctggcgcc +ggggcactgcagggccctcttgcttactgtatagtggtggcacgccgcct +gctggcagctagggacattgcagggtcctcttgctcaaggtgtagtggca +gcacgcccacctgctggcagctggggacactgccgggccctcttgctCCA +ACAGTACTGGCGGATTATAGGGAAACACCCGGAGCATATGCTGTTTGGTC +TCAGtagactcctaaatatgggattcctgggtttaaaagtaaaaaataaa +tatgtttaatttgtgaactgattaccatcagaattgtactgttctgtatc +ccaccagcaatgtctaggaatgcctgtttctccacaaagtgtttactttt +ggatttttgccagtctaacaggtgaAGccctggagattcttattagtgat +ttgggctggggcctggccatgtgtatttttttaaatttccactgatgatt +ttgctgcatggccggtgttgagaatgactgCGCAAATTTGCCGGATTTCC +TTTGCTGTTCCTGCATGTAGTTTAAACGAGATTGCCAGCACCGGGTATCA +TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTC +TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGT +CCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT +CATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCA +AGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG +TGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTT +AATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAG +CATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTGCTTGTGCTCATCT +CCTTGGCTGTGATACGTGGCCGGCCCTCGCTCCAGCAGCTGGACCCCTAC +CTGCCGTCTGCTGCCATCGGAGCCCAAAGCCGGGCTGTGACTGCTCAGAC +CAGCCGGCTGGAGGGAGGGGCTCAGCAGGTCTGGCTTTGGCCCTGGGAGA +GCAGGTGGAAGATCAGGCAGGCCATCGCTGCCACAGAACCCAGTGGATTG +GCCTAGGTGGGATCTCTGAGCTCAACAAGCCCTCTCTGGGTGGTAGGTGC +AGAGACGGGAGGGGCAGAGCCGCAGGCACAGCCAAGAGGGCTGAAGAAAT +GGTAGAACGGAGCAGCTGGTGATGTGTGGGCCCACCGGCCCCAGGCTCCT +GTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCA +GGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTG +AGTGTCCCCAGTGTTGCAGAGGTGAGAGGAGAGTAGACAGTGAGTGGGAG +TGGCGTCGCCCCTAGGGCTCTACGGGGCCGGCGTCTCCTGTCTCCTGGAG +AGGCTTCGATGCCCCTCCACACCCTCTTGATCTTCCCTGTGATGTCATCT +GGAGCCCTGCTGCTTGCGGTGGCCTATAAAGCCTCCTAGTCTGGCTCCAA +GGCCTGGCAGAGTCTTTCCCAGGGAAAGCTACAAGCAGCAAACAGTCTGC +ATGGGTCATCCCCTTCACTCCCAGCTCAGAGCCCAGGCCAGGGGCCCCCA +AGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCAT +AGGCAAGCCTGGCTGCCTCCAGCTGGGTCGACAGACAGGGGCTGGAGAAG +GGGAGAAGAGGAAAGTGAGGTTGCCTGCCCTGTCTCCTACCTGAGGCTGA +GGAAGGAGAAGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCT +TAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCAAAGGGATTCTG +CCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGAC +ACGCTGTTGGCCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGG +TTCTGCCATTGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCCT +AGAGCCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCC +AGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCT +GGCGCTGTGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATG +GGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTG +GAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGA +GAAAACAGGGGAATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGAT +CTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTGC +GTGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTT +GTCCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTG +CCCTTTCTATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAG +TCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTT +GTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTA +ACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAG +TTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACCACTTGAGCAAACT +CCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGG +CTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTT +TTTGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGC +CCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCT +GCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCCG +AGACGTTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGT +TGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGC +CTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAG +CACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCT +TCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTC +CCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGC +AACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACG +ATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGC +AGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTC +ACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTG +AGGGTGGTTGGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAAT +ACAGGAAGAAAAAGGCAGGACAGAATTACAAGGTGCTGGCCCAGGGCGGG +CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAG +ATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA +AGCCACAGACTGGGGTGAAGAGTTCAGTCACATGCGACCGGTGACTCCCT +GTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCC +AGTTAGCTCAGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCACTGATG +AGACAGCGGCTGTTTGAGGAGCCACCTCCCAGCCACCTCGGGGCCAGGGC +CAGGGTGTGCAGCAccactgtacaatggggaaactggcccagagaggtga +ggcagcttgcctggggtcacagagcaaggcaaaagcagcgctgggtacaa +gctcaAAACCATAGTGCCCAGGGCACTGCCGCTGCAGGCGCAGGCATCGC +ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAG +GCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC +ATTGCCTTGGACCGCTCTTGGCAGTCGAAGAAGATTCTCCTGTCAGTTTG +AGCTGGGTGAGCTTAGAGAGGAAAGCTCCACTATGGCTCCCAAACCAGGA +AGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGGTGGCGGCCCAG +GGCTTCCAGCATGTGCCCTAGGGGAAGCAGGGGCCAGCTGGCAAGAGCAG +GGGGTGGGCAGAAAGCACCCGGTGGACTCAGGGCTGGAGGGGAGGAGGCG +ATCTTGCCCAAGGCCCTCCGACTGCAAGCTCCAGGGCCCGCTCACCTtgc +tcctgctccttctgctgctgcttctccagctttcgctccttcatgctgcG +CAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAG +TGGCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGCTCCCTGGACTG +GAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGGG +CTGGGGAAGCTTACTGTGTCCAAGAGCCTGCTGGGAGGGAAGTCACCTCC +CCTCAAACGAGGAGCCCTGCGCTGGGGAGGCCGGACCTTTGGAGACTGTG +TGTGGGGGCCTGGGCACTGACTTCTGCAACCACCTGAGCGCGGGCATCCT +GTGTGCAGATACTCCCTGCTTCCTCTCTAGCCCCCACCCTGCAGAGCTGG +ACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTTGCACACACGAGCCAG +CAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTACACTGGGAGACAC +AGCAGTGAAGCTGAAATGAAAAATGTGTTGCTGTAGTTTGTTATTAGACC +CCTTCTTTCCATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTG +TTCAGGCTCCCTCTGCCCTAGAAGTGAGAAGTCCAGAGCTCTACAGTTTG +AAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGAAAC +TATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACCCACAGAAAATC +CACCCGAGTGCACTGAGCACGCCAGAAATCAGGTGGCCTCAAAGAGCTGC +TCCCACCTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCT +TGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAG +CACCTCAGGAGCtgggggtggtggtgggggcggtgggggtggtgTTAGTA +CCCCATCTTGTAGGTCTGAAACACAAAGTGTGGGGTGTCTAGGGAAGAAG +GTGTGTGACCAGGGAGGTCCCCGGCCCAGCTCCCATCCCAGAACCCAGCT +CACCTACCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCT +GGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAAT +GTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAA +CATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCT +GGGACCTGCAAGATTAGGCAGGGACATGTGAGAGGTGACAGGGACCTGCA +GGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGTGGAATAAGGGG +CCCAACAGCCTTGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTGC +ACCTGTCTCCACCTCTGTCCCACCCCTCCCACCTGCTGTTCCAGCTGCTC +TCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTG +CCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGG +AAGACATACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTG +ACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACA +GCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCC +CTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCA +CTAAGCCAGGCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGC +CATACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTG +ATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCTC +CGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAGAGG +GCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGCT +GCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGC +CCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTATATG +CGCGGCCAGCAGACCTGCAGGGCCCGCTCGTCCAGGGGGCGGTGCTTGCT +CTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCTGGGCGCCCG +TGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAGGGTACTTGGCA +CTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAGG +CTCAGAGGGCTAGGATTGCTTGGCAGGAGAGGGTGGAGTTGGAAGCCTGG +GCGAGAAGAAAGCTCAAGGTACAGGTGGGCAGCAGGGCAGAGACTGGGCA +GCCTCAGAGGCACGGGGAAATGGAGGGACTGCCCAGTAGCCTCAGGACAC +AGGGGTATGGGGACTACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTC +AATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGC +TCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACAG +AGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGA +GCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTAC +TTGCCAGGGCCGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATC +TGACCTGCAGGGTCGAGGAGTTGACGGTGCTGAGTTCCCTGCACTCTCAG +TAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCTGAAGGACAGCC +TCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTACTGAT +GGGGCAAGCACTTCACAACCCCTCATGATCACGTGCAGCAGACAATGTGG +CCTCTGCAGAGGGGGAACGGAGACCGGAGGCTGAGACTGGCAAGGCTGGA +CCTGAGTGTCGTCACCTAAATTCAGACGGGGAACTGCCCCTGCACATACT +GAACGGCTCACTGAGCAAACCCCGAGTCCCGACCACCGCCTCAGTGTGGT +CTAGCTcctcacctgcttccatcctccctggtgcggggtgggcccagtga +tatcagctgcctgctgttccccagatgtgccaagtgcattcttgtgtgct +tgcatctcatggaacgccatttccccagacatccctgtggctggctccTG +ATGCCCGAGGCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCAT +GCTTTTCCATGTTCTTTGGCCGCAGCAAGGCCGCTCTCACTGCAAAGTTA +ACTCTGATGCGTGTGTAACACAACATCCTCCTCCCAGTCGCCCCTGTAGC +TCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCACACTCCACGT +GCAGAGCAGCCTCAGCACTCACCGGGCACGAGCGAGCCTGTGTGGTGCGC +AGGGATGAGAAGGCAGAGGCGCGACTGGGGTTCATGAGGAAGGGCAGGAG +GAGGGTGTGGGATGGTGGAGGGGTTTGAGAAGGCAGAGGCGCGACTGGGG +TTCATGAGGAAAGGGAGGGGGAGGATGTGGGATGGTGGAGGGGCTGCAGA +CTCTGGGCTAGGGAAAGCTGGGATGTCTCTAAAGGTTGGAATGAATGGCC +TAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAACGTTAGAAGGCC +TTGGCCCCCAGAGAGCCAATTTCACAATCCAGAAGTCCCCGTGCCCTAAA +GGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCAT +GGCAGGGCTGGGAGTACCAGCAGGCACTCAAGCGGCTTAAGTGTTCCATG +ACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCAC +CATCTCCTTCCAGTGAGGAAGCGGGACCACCACCCAGCGTGTGCTCCATC +TTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCAC +AAGCTGTCTTAATTGACCCTAGTTCCCAGGGCAGCCTCGTTCTGCCTTGG +GTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCCAC +AGGGGCAGTGGGAGGGAACTGagactggggagggacaaaggctgctctgt +cctggtgctcccacaaaggagaagggctgatcactcaaagttgcgaacac +caagctcaacaatgagccctggaaaatttctggaatggattattaaacag +agagtctgtaagcacttagaaaaggccgcggtgagtcccaggggccagca +ctgctcgaaatgtacagcatttctctttgtaacaggattattagcctgct +gtgcccggggaaaacatgcagcacagtgcatctcgagtcagcaggatttt +gacggcttctaacaaaatcttgtagacaagatggagctatgggggttgga +ggagagaacatataggaaaaatcagagccaaatgaaccacagccccaaag +ggcacagttgaacaatggactgattccagccttgcacggagggatctggc +agagtCCATCCAGTTCATTCAACACCTGGTTAGAAAACTGGGGCCAGCAC +ACAGGGGAAGGGTAAGCTGGTTTCATGATCGAATCAAGGCTCAGACAATT +TTTAAAGGCCAGAGGGTAGACTGCAATCACcaagatgaaatttacaagga +acaaatgtgaagcccaacatttaggttttaaaaatcaagcgtataaatac +agaaggtggagggaacttgctttagacacagttcaggtgaagaaagacct +ggaaacttctgttaactataagctcagtaGGGGCTAAAAGCATGTTAATC +GGCATAAAAAGGCAATGAGATCTTAGGGCACACAGCTCCCCGCCCCTCTT +CTGCCCTTCATCCTTCTTTCAATCAGCAGGGACCGTGCACTCTCTTGGAG +CCACCACAGAAAACAGAGGTGCATCCAGCACCACAGAAAACAGAGCCACC +ACAGAAAACAGAGGGTGACTGTCATCCCCTCCAGTCTCTGCACACTCCCA +GCTGCAGCAGAGCAGGAGGAGAGAGCACAGCCTGCAATGCTAATTTGCCA +GGAGCTCACCTGCCTGCGTCACTGGGCACAGACGCCAGTGAGGCCAGAGG +CCGGGCTGTGCTGGGGCCTGAGCCGGGTGGTGGGGAGAGAGTCTCTCCCC +TGCCCCTGTCTCTTCCGTGCAGGAGGAGCATGTTTAAGGGGACGGGTTCA +AAGCTGGTCACATCCCCACCGAAAAAGCCCATGGACAACGAAAAGCCCAC +TAGCTTGTCCAGTGCCACAGGAGGGGCAAGTGGAGGAGGAGAGGTGGCGG +TGCTCCCCACTCCACTGCCAGTCGTCACTGGCTCTCCCTTCCCTTCATCC +TCGTTCCCTATCTGTCACCATTTCCTGTCGTCGTTTCCTCTGAATGTCTC +ACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTC +GTATCCTGACTACAATAACAGCTTCTGGGTGTCCCTGGCATCCACTCTCT +CTCCCTTCTTGTCCCTTCCGTGACGGATGCCTGAGGAACCTTCCCCAAAC +TCTTCTGTCCCATCCCTGCCCTGCTCAAAATCCAATCACAGCTCCCTAAC +ACGCCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCCGTGGGCCCTAAC +TCACTCATCCCAACTCTTCACTCACTGCCCTGCCCCACACCCTGCCAGGG +AGCCTCCCGTGGCACCGTGGGGACACAAAGGAACCAGGGCAAAGCTCCCT +CAGCCCCATTCAAAGAGGCCTGGCCCACAGGCTCACGGAAAGTCAGCCTC +TCATGCCCCGAGAGCTGAGTGCAAGGGAGAGGCAGCGCTGTCTGTGCTTC +CCATGCAGAAGCACCCCCCTCCCACCCCTGTGCAGGCCGGCCTTCGCGGC +AGACCACCATACACCACGTTCCAAGCCACACTGAGGCCTCCCTCCAAGCC +TGCAGCCCCCATTTCCAGACCCTGCCAGGGCAACCTGCATATCCACCTCC +CTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCACgt +ggttttcctcttcagcaactatttcctttttactcaagcaatggccccat +ttcccttggggaatccatctctctcgcaggcttagtcccagagcttcagg +tggggctgcccacagagctcctcagTCTAAGCCAAGTGGTGTGTCATAGT +CCCCTGGCCCCATTAATGGATTCTGGGATAGACATGAGGACCAAGCCAGG +TGGGATGAGTGAGTGTGGCTTCTGGAGGAAGTGGGGACACAGGACAGCAT +TCTTTCCTGCTGGACCTGACCCTGTGTCATGTCACCTTGCTACCACGAGA +GCATGGCCTGTCTGGGAATGCAGCCAGACCCAAAGAAGCAAACTGACATG +GAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCCG +AAGGCTGCTCTACTGATTGGTTAATTTTTGCTTAGCTTGGTCTGGGGAGT +TCTGACAGGCGTGCCACCAATTCTTACCGATTTCTCTCCACTCTAGACCC +TGAGAAGCCCACGCGGTTCATGCTAGCAATTAACAATCAATCTCGCCCTA +TGTGTTCCCATTCCAGCCTCTAGGACACAGTGGCAGCCACATAATTGGTA +TCTCTTAAGGTCCAGCACGAGGTGGAGCACATGGTGGAGAGACAGATGCA +GTGACCTGGAACCCAGGAGTGAGGGAGCCAGGACTCAGGCCCAAGGCTCC +TGAGAGGCATCTGGCCCTCCCTGCGCTGTGCCAGCAGCTTGGAGAACCCA +CACTCAATGAACGCAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTC +TCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCA +AGTACCAGGACAGGAAAGGAAAGACGCCAAAAATCCAGCGCTGCCCTCAG +AGAAGGGCAACCACGCAGTCCCCATCTTGGCAAGGAAACACAATTTCCGA +GGGAATGGTTTTGGCCTCCATTCTAAGTGCTGGACATGGGGTGGCCATAA 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