This commit is contained in:
commit
ebb27556b5
3
.gitignore
vendored
3
.gitignore
vendored
@ -212,3 +212,6 @@ pyrightconfig.json
|
||||
|
||||
# Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
|
||||
|
||||
output
|
||||
!docs
|
||||
docs/build
|
||||
26
.vscode/launch.json
vendored
Normal file
26
.vscode/launch.json
vendored
Normal file
@ -0,0 +1,26 @@
|
||||
{
|
||||
// Use IntelliSense to learn about possible attributes.
|
||||
// Hover to view descriptions of existing attributes.
|
||||
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
|
||||
"version": "0.2.0",
|
||||
"configurations": [
|
||||
{
|
||||
"name": "Python: Module",
|
||||
"type": "python",
|
||||
"request": "launch",
|
||||
"module": "bmlsa.cli",
|
||||
"args": [
|
||||
"-I",
|
||||
"id",
|
||||
"-S",
|
||||
"sequence",
|
||||
"-B",
|
||||
"BLASTp",
|
||||
"${workspaceFolder}/tests/resources/SARS_CoV-2_genes.csv",
|
||||
"${workspaceFolder}/tests/resources/NC_045512_coding.fasta",
|
||||
"${workspaceFolder}/output"
|
||||
],
|
||||
"justMyCode": true
|
||||
}
|
||||
]
|
||||
}
|
||||
11
.vscode/settings.json
vendored
11
.vscode/settings.json
vendored
@ -1,3 +1,12 @@
|
||||
{
|
||||
"python.formatting.provider": "black"
|
||||
"python.formatting.provider": "black",
|
||||
"cSpell.words": [
|
||||
"Biopython",
|
||||
"BLOSUM",
|
||||
"bmlsa",
|
||||
"FASTA"
|
||||
],
|
||||
"python.testing.pytestEnabled": true,
|
||||
"python.analysis.inlayHints.pytestParameters": true,
|
||||
"autoDocstring.docstringFormat": "sphinx"
|
||||
}
|
||||
23
Jenkinsfile
vendored
23
Jenkinsfile
vendored
@ -1,26 +1,33 @@
|
||||
pipeline {
|
||||
agent any
|
||||
stages {
|
||||
stage("clean") {
|
||||
steps {
|
||||
sh 'rm -rf ./dist/*'
|
||||
}
|
||||
}
|
||||
stage("install") {
|
||||
steps {
|
||||
sh 'mamba env update --file environment.yml'
|
||||
sh 'mamba env update --file environment.yml || mamba env create --force --file environment.yml'
|
||||
sh 'echo "mamba activate bmlsa" >> ~/.bashrc'
|
||||
}
|
||||
}
|
||||
stage("unit tests") {
|
||||
steps {
|
||||
sh "python -m pytest --junitxml=test_results.xml"
|
||||
xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)]
|
||||
}
|
||||
}
|
||||
stage("build") {
|
||||
steps {
|
||||
sh 'rm -rf ./dist/*'
|
||||
sh 'rm -rf ./docs/build/*'
|
||||
sh "python -m build"
|
||||
sh 'sphinx-apidoc -o docs/source/ src/bmlsa --force'
|
||||
sh 'make -C docs html'
|
||||
publishHTML([allowMissing: false, alwaysLinkToLastBuild: false, keepAll: false, reportDir: 'docs/build/html', reportFiles: 'index.html', reportName: 'Documentation', reportTitles: ''])
|
||||
}
|
||||
}
|
||||
stage("test") {
|
||||
stage("test installation") {
|
||||
steps {
|
||||
sh "pip install dist/*.whl"
|
||||
sh "pip install dist/*.whl --force-reinstall"
|
||||
sh "bmlsa -h"
|
||||
sh "bmlsa -I id -S sequence -B BLASTp tests/resources/SARS_CoV-2_genes.csv tests/resources/NC_045512_coding.fasta ./output/"
|
||||
}
|
||||
}
|
||||
stage("archive") {
|
||||
|
||||
17
README.md
17
README.md
@ -1,3 +1,18 @@
|
||||
[](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/master/)
|
||||
|
||||
# BMLSA
|
||||
|
||||
A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm
|
||||
A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm.
|
||||
|
||||
## Features
|
||||
|
||||
- Aligns a CSV of short sequences locally to a given reference sequence
|
||||
- Outputs in a CSV with old and new positions
|
||||
- Selectable parameters for alignment
|
||||
- Compatible with broad-range of input CSV formats
|
||||
- Automatically align with all sequences in reference FASTA
|
||||
- All produced output is human readable!
|
||||
|
||||
## More Information
|
||||
|
||||
For all live downloadable artifacts, build statuses, unit test results, and documentation, check out the continuous integration page for the [master branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/master/) ([development branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/develop/)).
|
||||
@ -1,42 +0,0 @@
|
||||
from Bio.Align import PairwiseAligner, substitution_matrices
|
||||
from bmlsa.datatypes import AlignedSequence
|
||||
from bmlsa.exceptions import UnexpectedAlignmentResult
|
||||
|
||||
|
||||
def protein_align_many_to_one_ssw(sequence: str, queries: dict[str, AlignedSequence]):
|
||||
annotation_pairs = {}
|
||||
aligner = PairwiseAligner()
|
||||
aligner.mode = "local"
|
||||
aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
|
||||
aligner.extend_gap_score = -1
|
||||
aligner.open_gap_score = -11
|
||||
for id, query in queries.items():
|
||||
try:
|
||||
alignments = aligner.align(sequence, query.sequence)
|
||||
except ValueError:
|
||||
continue
|
||||
if len(alignments) > 1:
|
||||
raise UnexpectedAlignmentResult(
|
||||
"More than one alignment resulted from a single query."
|
||||
)
|
||||
for alignment in alignments:
|
||||
score, query_aligned = (alignment.score, alignment.aligned[0][0])
|
||||
aligned_start, aligned_end = query_aligned
|
||||
annotation_pairs[id] = AlignedSequence(
|
||||
id,
|
||||
query.sequence,
|
||||
query.name,
|
||||
query.description,
|
||||
query.start,
|
||||
query.end,
|
||||
query.score,
|
||||
), AlignedSequence(
|
||||
id,
|
||||
alignment.query,
|
||||
query.name,
|
||||
query.description,
|
||||
int(aligned_start) + 1,
|
||||
aligned_end,
|
||||
score,
|
||||
)
|
||||
return annotation_pairs
|
||||
94
bmlsa/cli.py
94
bmlsa/cli.py
@ -1,94 +0,0 @@
|
||||
import os
|
||||
import argparse
|
||||
from Bio import SeqIO
|
||||
from bmlsa.aligner import protein_align_many_to_one_ssw
|
||||
|
||||
from bmlsa.persistence import read_annotations_from_csv, save_alignments_to_csv
|
||||
|
||||
|
||||
def main():
|
||||
argparser = argparse.ArgumentParser("blmsa")
|
||||
argparser.add_argument(
|
||||
"annotations",
|
||||
type=str,
|
||||
help=(
|
||||
"Path to CSV containing the sequences to align as well as the "
|
||||
"annotations for the respective sequences"
|
||||
),
|
||||
metavar="a",
|
||||
)
|
||||
argparser.add_argument(
|
||||
"sequence",
|
||||
type=str,
|
||||
help=(
|
||||
"Path to the sequence to annotate in FASTA format. "
|
||||
"If multiple sequences are present, annotations will be run on each"
|
||||
),
|
||||
metavar="s",
|
||||
)
|
||||
argparser.add_argument(
|
||||
"output", type=str, help="Path to output location", metavar="o"
|
||||
)
|
||||
argparser.add_argument(
|
||||
"-I", "--id-header", type=str, help="The header for the ID of the annotation"
|
||||
)
|
||||
argparser.add_argument(
|
||||
"-N",
|
||||
"--name-header",
|
||||
type=str,
|
||||
help="The header for the name of the annotation",
|
||||
required=False,
|
||||
)
|
||||
argparser.add_argument(
|
||||
"-D",
|
||||
"--desc-header",
|
||||
type=str,
|
||||
help="The header for the description of the annotation",
|
||||
required=False,
|
||||
)
|
||||
argparser.add_argument(
|
||||
"-T",
|
||||
"--start-header",
|
||||
type=str,
|
||||
help="The header for the start of the annotation",
|
||||
required=False,
|
||||
)
|
||||
argparser.add_argument(
|
||||
"-E",
|
||||
"--end-header",
|
||||
type=str,
|
||||
help="The header for the end of the annotation",
|
||||
required=False,
|
||||
)
|
||||
argparser.add_argument(
|
||||
"-S",
|
||||
"--seq-header",
|
||||
type=str,
|
||||
help="The header for the sequence of the annotation",
|
||||
)
|
||||
args = argparser.parse_args()
|
||||
given_annotations = read_annotations_from_csv(
|
||||
args.annotations,
|
||||
args.id_header,
|
||||
args.name_header,
|
||||
args.desc_header,
|
||||
args.start_header,
|
||||
args.end_header,
|
||||
args.seq_header,
|
||||
)
|
||||
with open(args.sequence, "r") as sequence_fd:
|
||||
for sequence in SeqIO.parse(sequence_fd, "fasta"):
|
||||
aligned_annotations = protein_align_many_to_one_ssw(
|
||||
str(sequence.seq), given_annotations
|
||||
)
|
||||
save_alignments_to_csv(
|
||||
aligned_annotations,
|
||||
os.path.join(
|
||||
args.output,
|
||||
sequence.id.replace("|", "+").replace(".", "_") + ".csv",
|
||||
),
|
||||
)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
@ -1,46 +0,0 @@
|
||||
class AlignedSequence:
|
||||
def __init__(
|
||||
self,
|
||||
id: str,
|
||||
sequence: str,
|
||||
name: str = None,
|
||||
description: str = None,
|
||||
start: int = None,
|
||||
end: int = None,
|
||||
score: int = None,
|
||||
) -> None:
|
||||
self._description = description
|
||||
self._start = start
|
||||
self._end = end
|
||||
self._id = id
|
||||
self._name = name
|
||||
self._sequence = sequence
|
||||
self._score = score
|
||||
|
||||
@property
|
||||
def start(self):
|
||||
return self._start
|
||||
|
||||
@property
|
||||
def end(self):
|
||||
return self._end
|
||||
|
||||
@property
|
||||
def id(self):
|
||||
return self._id
|
||||
|
||||
@property
|
||||
def name(self):
|
||||
return self._name
|
||||
|
||||
@property
|
||||
def description(self):
|
||||
return self._description
|
||||
|
||||
@property
|
||||
def sequence(self):
|
||||
return self._sequence
|
||||
|
||||
@property
|
||||
def score(self):
|
||||
return self._score
|
||||
20
docs/Makefile
Normal file
20
docs/Makefile
Normal file
@ -0,0 +1,20 @@
|
||||
# Minimal makefile for Sphinx documentation
|
||||
#
|
||||
|
||||
# You can set these variables from the command line, and also
|
||||
# from the environment for the first two.
|
||||
SPHINXOPTS ?=
|
||||
SPHINXBUILD ?= sphinx-build
|
||||
SOURCEDIR = source
|
||||
BUILDDIR = build
|
||||
|
||||
# Put it first so that "make" without argument is like "make help".
|
||||
help:
|
||||
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
|
||||
|
||||
.PHONY: help Makefile
|
||||
|
||||
# Catch-all target: route all unknown targets to Sphinx using the new
|
||||
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
|
||||
%: Makefile
|
||||
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
|
||||
35
docs/make.bat
Normal file
35
docs/make.bat
Normal file
@ -0,0 +1,35 @@
|
||||
@ECHO OFF
|
||||
|
||||
pushd %~dp0
|
||||
|
||||
REM Command file for Sphinx documentation
|
||||
|
||||
if "%SPHINXBUILD%" == "" (
|
||||
set SPHINXBUILD=sphinx-build
|
||||
)
|
||||
set SOURCEDIR=source
|
||||
set BUILDDIR=build
|
||||
|
||||
%SPHINXBUILD% >NUL 2>NUL
|
||||
if errorlevel 9009 (
|
||||
echo.
|
||||
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
|
||||
echo.installed, then set the SPHINXBUILD environment variable to point
|
||||
echo.to the full path of the 'sphinx-build' executable. Alternatively you
|
||||
echo.may add the Sphinx directory to PATH.
|
||||
echo.
|
||||
echo.If you don't have Sphinx installed, grab it from
|
||||
echo.https://www.sphinx-doc.org/
|
||||
exit /b 1
|
||||
)
|
||||
|
||||
if "%1" == "" goto help
|
||||
|
||||
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
|
||||
goto end
|
||||
|
||||
:help
|
||||
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
|
||||
|
||||
:end
|
||||
popd
|
||||
53
docs/source/bmlsa.rst
Normal file
53
docs/source/bmlsa.rst
Normal file
@ -0,0 +1,53 @@
|
||||
bmlsa package
|
||||
=============
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
bmlsa.aligner module
|
||||
--------------------
|
||||
|
||||
.. automodule:: bmlsa.aligner
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
bmlsa.cli module
|
||||
----------------
|
||||
|
||||
.. automodule:: bmlsa.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
bmlsa.datatypes module
|
||||
----------------------
|
||||
|
||||
.. automodule:: bmlsa.datatypes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
bmlsa.exceptions module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: bmlsa.exceptions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
bmlsa.io module
|
||||
---------------
|
||||
|
||||
.. automodule:: bmlsa.io
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Module contents
|
||||
---------------
|
||||
|
||||
.. automodule:: bmlsa
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
33
docs/source/conf.py
Normal file
33
docs/source/conf.py
Normal file
@ -0,0 +1,33 @@
|
||||
import os
|
||||
import sys
|
||||
|
||||
# Configure system path
|
||||
|
||||
sys.path.insert(0, os.path.abspath("../src/"))
|
||||
|
||||
# Configuration file for the Sphinx documentation builder.
|
||||
#
|
||||
# For the full list of built-in configuration values, see the documentation:
|
||||
# https://www.sphinx-doc.org/en/master/usage/configuration.html
|
||||
|
||||
# -- Project information -----------------------------------------------------
|
||||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
|
||||
|
||||
project = "BMLSA"
|
||||
copyright = "2023, Harrison"
|
||||
author = "Harrison"
|
||||
|
||||
# -- General configuration ---------------------------------------------------
|
||||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
|
||||
|
||||
extensions = ["sphinx.ext.autodoc"]
|
||||
|
||||
templates_path = ["_templates"]
|
||||
exclude_patterns = []
|
||||
|
||||
|
||||
# -- Options for HTML output -------------------------------------------------
|
||||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
|
||||
|
||||
html_theme = "alabaster"
|
||||
html_static_path = ["_static"]
|
||||
21
docs/source/index.rst
Normal file
21
docs/source/index.rst
Normal file
@ -0,0 +1,21 @@
|
||||
.. BMLSA documentation master file, created by
|
||||
sphinx-quickstart on Fri Apr 28 13:04:16 2023.
|
||||
You can adapt this file completely to your liking, but it should at least
|
||||
contain the root `toctree` directive.
|
||||
|
||||
Welcome to BMLSA's documentation!
|
||||
=================================
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
:caption: Contents:
|
||||
|
||||
modules
|
||||
|
||||
|
||||
Indices and tables
|
||||
==================
|
||||
|
||||
* :ref:`genindex`
|
||||
* :ref:`modindex`
|
||||
* :ref:`search`
|
||||
7
docs/source/modules.rst
Normal file
7
docs/source/modules.rst
Normal file
@ -0,0 +1,7 @@
|
||||
bmlsa
|
||||
=====
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
bmlsa
|
||||
@ -3,6 +3,9 @@ channels:
|
||||
- conda-forge
|
||||
dependencies:
|
||||
- biopython=1.81
|
||||
- build=0.7
|
||||
- pytest=7
|
||||
- pytest=7.3
|
||||
- hypothesis=6.56
|
||||
- twine=4
|
||||
- python-build=0.10.0
|
||||
- setuptools=67.6
|
||||
- sphinx=6.2
|
||||
@ -1,12 +1,17 @@
|
||||
[metadata]
|
||||
name = bmlsa
|
||||
version = 0.0.3
|
||||
version = 0.0.4
|
||||
|
||||
[options]
|
||||
packages = bmlsa
|
||||
package_dir =
|
||||
= src
|
||||
install_requires =
|
||||
biopython ==1.81
|
||||
|
||||
[options.entry_points]
|
||||
console_scripts =
|
||||
bmlsa = bmlsa.cli:main
|
||||
|
||||
[tool:pytest]
|
||||
pythonpath = src
|
||||
testpaths = tests
|
||||
68
src/bmlsa/aligner.py
Normal file
68
src/bmlsa/aligner.py
Normal file
@ -0,0 +1,68 @@
|
||||
import logging
|
||||
from typing import Generator, Iterable
|
||||
from Bio.Align import PairwiseAligner, substitution_matrices
|
||||
from bmlsa.datatypes import QuerySequence
|
||||
|
||||
logger = logging.getLogger(__name__)
|
||||
|
||||
|
||||
def align_many_to_one_ssw(
|
||||
reference_sequence: str,
|
||||
queries: Iterable[QuerySequence],
|
||||
extend_gap_score: int,
|
||||
open_gap_score: int,
|
||||
alignment_mode: str,
|
||||
substitution_matrix: str = "BLOSUM62",
|
||||
) -> Generator[tuple[QuerySequence, QuerySequence], None, None]:
|
||||
"""Aligns :obj:`bmlsa.datatypes.QuerySequence` objects to a given reference sequence
|
||||
|
||||
:param reference_sequence: The reference sequence to align to
|
||||
:type reference_sequence: str
|
||||
:param queries: A iterable sequence of :obj:`bmlsa.datatypes.QuerySequence`
|
||||
:type queries: Iterable[QuerySequence]
|
||||
:param extend_gap_score: The gap score to use for alignment. Typically negative.
|
||||
:type extend_gap_score: int
|
||||
:param open_gap_score: The open gap score to use for alignment. Typically negative.
|
||||
:type open_gap_score: int
|
||||
:param alignment_mode: The alignment mode to use. Either "local" or "global".
|
||||
:type alignment_mode: str
|
||||
:param substitution_matrix: The name of the substitution matrix available in :mod:`Bio.Align`, defaults to "BLOSUM62"
|
||||
:type substitution_matrix: str, optional
|
||||
:yield: Pairs of :obj:`bmlsa.datatypes.QuerySequence` objects where the first is the original, and the second is the aligned version
|
||||
:rtype: a generator of :obj:`bmlsa.datatypes.QuerySequence` objects
|
||||
"""
|
||||
# TODO Consider using the built in "scoring" parameter
|
||||
aligner = PairwiseAligner()
|
||||
aligner.substitution_matrix = substitution_matrices.load(substitution_matrix)
|
||||
aligner.extend_gap_score = extend_gap_score
|
||||
aligner.open_gap_score = open_gap_score
|
||||
aligner.mode = alignment_mode
|
||||
for query in queries:
|
||||
try:
|
||||
alignments = aligner.align(reference_sequence, query.sequence)
|
||||
except ValueError:
|
||||
logger.warning(
|
||||
'Skipping sequence with id "%s" due to invalid characters', query.id
|
||||
)
|
||||
continue
|
||||
# TODO Implement comparison with input positions to choose best
|
||||
for alignment in alignments:
|
||||
score, query_aligned = (alignment.score, alignment.aligned[0][0])
|
||||
aligned_start, aligned_end = query_aligned
|
||||
yield QuerySequence(
|
||||
query.id,
|
||||
query.sequence,
|
||||
query.name,
|
||||
query.description,
|
||||
query.start,
|
||||
query.end,
|
||||
query.score,
|
||||
), QuerySequence(
|
||||
query.id,
|
||||
alignment.query,
|
||||
query.name,
|
||||
query.description,
|
||||
int(aligned_start) + 1,
|
||||
aligned_end,
|
||||
score,
|
||||
)
|
||||
195
src/bmlsa/cli.py
Normal file
195
src/bmlsa/cli.py
Normal file
@ -0,0 +1,195 @@
|
||||
import os
|
||||
import argparse
|
||||
from Bio import SeqIO
|
||||
import logging
|
||||
from bmlsa.aligner import align_many_to_one_ssw
|
||||
|
||||
from bmlsa.io import queries_from_csv, save_alignments_to_csv
|
||||
|
||||
logger = logging.getLogger(__name__)
|
||||
|
||||
DEFAULT_ALIGNMENT_PARAMETERS = {
|
||||
"BLASTp": {
|
||||
"extend_gap_score": -1,
|
||||
"open_gap_score": -11,
|
||||
"substitution_matrix": "BLOSUM62",
|
||||
"alignment_mode": "local",
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
def run(args):
|
||||
if (
|
||||
not (args.extend_gap_score and args.open_gap_score and args.alignment_mode)
|
||||
and not args.behave_as
|
||||
):
|
||||
logger.error(
|
||||
'Must either specify all of "--extend-gap-score", "--open-gap-score", '
|
||||
'"--alignment-mode", or, at least "--behave-as". See help (-h) for '
|
||||
"more information."
|
||||
)
|
||||
exit(3)
|
||||
queries = queries_from_csv(
|
||||
args.queries,
|
||||
args.id_header,
|
||||
args.seq_header,
|
||||
args.name_header,
|
||||
args.desc_header,
|
||||
args.start_header,
|
||||
args.end_header,
|
||||
)
|
||||
|
||||
if args.behave_as and args.behave_as not in DEFAULT_ALIGNMENT_PARAMETERS:
|
||||
logger.error('"--behave-as" received bad option.')
|
||||
exit(3)
|
||||
|
||||
scoring_parameter = (
|
||||
{
|
||||
"extend_gap_score": args.extend_gap_score,
|
||||
"open_gap_score": args.open_gap_score,
|
||||
"alignment_mode": args.alignment_mode,
|
||||
"substitution_matrix": args.substitution_matrix
|
||||
if args.substitution_matrix is not None
|
||||
else "BLOSUM62",
|
||||
}
|
||||
if args.behave_as not in DEFAULT_ALIGNMENT_PARAMETERS
|
||||
else DEFAULT_ALIGNMENT_PARAMETERS[args.behave_as]
|
||||
)
|
||||
|
||||
os.makedirs(args.output, exist_ok=True)
|
||||
with open(args.sequence, "r") as sequence_fd:
|
||||
for sequence in SeqIO.parse(sequence_fd, "fasta"):
|
||||
aligned_queries = align_many_to_one_ssw(
|
||||
str(sequence.seq), queries, **scoring_parameter
|
||||
)
|
||||
save_alignments_to_csv(
|
||||
aligned_queries,
|
||||
os.path.join(
|
||||
args.output,
|
||||
sequence.id.replace("|", "+").replace(".", "_") + ".csv",
|
||||
),
|
||||
)
|
||||
|
||||
|
||||
def main():
|
||||
arg_parser = argparse.ArgumentParser("bmlsa")
|
||||
arg_parser.add_argument(
|
||||
"queries",
|
||||
type=str,
|
||||
help=(
|
||||
"Path to CSV containing the sequences to align as well as the "
|
||||
"queries for the respective sequences."
|
||||
),
|
||||
metavar="a",
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"sequence",
|
||||
type=str,
|
||||
help=(
|
||||
"Path to the sequence to use as reference in FASTA format. "
|
||||
"If multiple sequences are present in the same FASTA file, "
|
||||
"each will be used as a separate reference sequence for separate "
|
||||
"runs automatically."
|
||||
),
|
||||
metavar="s",
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"output", type=str, help="Path to output location", metavar="o"
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-I",
|
||||
"--id-header",
|
||||
type=str,
|
||||
help="The header of the column for the ID of the sequence to align to "
|
||||
"the reference sequence.",
|
||||
required=True,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-N",
|
||||
"--name-header",
|
||||
type=str,
|
||||
help="The header of the column for the name of the sequence to align to "
|
||||
"the reference sequence.",
|
||||
required=False,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-D",
|
||||
"--desc-header",
|
||||
type=str,
|
||||
help="The header of the column for the description of the sequence to "
|
||||
"align to the reference sequence.",
|
||||
required=False,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-T",
|
||||
"--start-header",
|
||||
type=str,
|
||||
help="The header of the column for the start position of the sequence to "
|
||||
"align to the reference sequence.",
|
||||
required=False,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-E",
|
||||
"--end-header",
|
||||
type=str,
|
||||
help="The header of the column for end position of the sequence to "
|
||||
"align to the reference sequence.",
|
||||
required=False,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-S",
|
||||
"--seq-header",
|
||||
type=str,
|
||||
help="The header of the column for the actual sequence to align to the "
|
||||
"reference sequence.",
|
||||
required=True,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-e",
|
||||
"--extend-gap-score",
|
||||
type=int,
|
||||
help="The scoring for extending a gap.",
|
||||
required=False,
|
||||
default=None,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-o",
|
||||
"--open-gap-score",
|
||||
type=int,
|
||||
help="The scoring for opening a gap.",
|
||||
required=False,
|
||||
default=None,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-M",
|
||||
"--alignment-mode",
|
||||
type=str,
|
||||
help="The alignment mode.",
|
||||
choices=["local", "global"],
|
||||
required=False,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-m",
|
||||
"--substitution-matrix",
|
||||
type=str,
|
||||
help="The name of the substitution matrix.",
|
||||
required=False,
|
||||
default=None,
|
||||
)
|
||||
arg_parser.add_argument(
|
||||
"-B",
|
||||
"--behave-as",
|
||||
type=str,
|
||||
help="Use built-in parameters for alignment scoring. If this is specified "
|
||||
"along either of the scoring arguments, the alignment parameter arguments "
|
||||
'("--open-gap-score" and/or "--extend-gab-score" and "--alignment-mode") '
|
||||
"will override any defaults set by this argument.",
|
||||
required=False,
|
||||
default=None,
|
||||
)
|
||||
args = arg_parser.parse_args()
|
||||
run(args)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
65
src/bmlsa/datatypes.py
Normal file
65
src/bmlsa/datatypes.py
Normal file
@ -0,0 +1,65 @@
|
||||
class QuerySequence:
|
||||
"""Represents a sequence that may be aligned."""
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
id: str,
|
||||
sequence: str,
|
||||
name: str = None,
|
||||
description: str = None,
|
||||
start: int = None,
|
||||
end: int = None,
|
||||
score: int = None,
|
||||
) -> None:
|
||||
"""Instantiates a :obj:bmlsa.datatypes.QuerySequence object
|
||||
|
||||
:param id: The id of the query sequence
|
||||
:type id: str
|
||||
:param sequence: The sequence itself
|
||||
:type sequence: str
|
||||
:param name: The name of the sequence, defaults to None
|
||||
:type name: str, optional
|
||||
:param description: The description of the sequence, defaults to None
|
||||
:type description: str, optional
|
||||
:param start: The start of the sequence, defaults to None
|
||||
:type start: int, optional
|
||||
:param end: The end of the sequence, defaults to None
|
||||
:type end: int, optional
|
||||
:param score: The alignment score of the sequence, defaults to None
|
||||
:type score: int, optional
|
||||
"""
|
||||
self._description = description
|
||||
self._start = start
|
||||
self._end = end
|
||||
self._id = id
|
||||
self._name = name
|
||||
self._sequence = sequence.replace("\n", "").replace("\r", "")
|
||||
self._score = score
|
||||
|
||||
@property
|
||||
def start(self):
|
||||
return self._start
|
||||
|
||||
@property
|
||||
def end(self):
|
||||
return self._end
|
||||
|
||||
@property
|
||||
def id(self):
|
||||
return self._id
|
||||
|
||||
@property
|
||||
def name(self):
|
||||
return self._name
|
||||
|
||||
@property
|
||||
def description(self):
|
||||
return self._description
|
||||
|
||||
@property
|
||||
def sequence(self):
|
||||
return self._sequence
|
||||
|
||||
@property
|
||||
def score(self):
|
||||
return self._score
|
||||
@ -1,44 +1,63 @@
|
||||
import csv
|
||||
from typing import Generator, Iterable
|
||||
|
||||
from bmlsa.datatypes import AlignedSequence
|
||||
from bmlsa.datatypes import QuerySequence
|
||||
|
||||
|
||||
def read_annotations_from_csv(
|
||||
def queries_from_csv(
|
||||
csv_path: str,
|
||||
id_header: str,
|
||||
name_header: str,
|
||||
desc_header: str,
|
||||
start_header: str,
|
||||
end_header: str,
|
||||
sequence_header: str,
|
||||
):
|
||||
annotations = {}
|
||||
name_header: str = None,
|
||||
desc_header: str = None,
|
||||
start_header: str = None,
|
||||
end_header: str = None,
|
||||
) -> Generator[QuerySequence, None, None]:
|
||||
"""Generates and :obj:`bmlsa.datatypes.QuerySequence` instances from a CSV file.
|
||||
|
||||
:param csv_path: Path to CSV to use
|
||||
:type csv_path: str
|
||||
:param id_header: The column title for the unique identifier for each query sequence
|
||||
:type id_header: str
|
||||
:param sequence_header: The column title for the sequences themselves
|
||||
:type sequence_header: str
|
||||
:param name_header: The column title for the name of the sequence, defaults to None
|
||||
:type name_header: str, optional
|
||||
:param desc_header: The column title for the description of the sequence, defaults to None
|
||||
:type desc_header: str, optional
|
||||
:param start_header: The column title for the start position of the sequence, defaults to None
|
||||
:type start_header: str, optional
|
||||
:param end_header: The column title for the end position of the sequence, defaults to None
|
||||
:type end_header: str, optional
|
||||
:yield: One :obj:`bmlsa.datatypes.QuerySequence` for each row
|
||||
:rtype: A generator that yields objects of :class:`bmlsa.datatypes.QuerySequence`
|
||||
"""
|
||||
with open(csv_path, "r") as csv_fd:
|
||||
reader = csv.reader(csv_fd)
|
||||
id_ind = None
|
||||
sequence_ind = None
|
||||
name_ind = None
|
||||
desc_ind = None
|
||||
start_ind = None
|
||||
end_ind = None
|
||||
sequence_ind = None
|
||||
headers_parsed = False
|
||||
for row in reader:
|
||||
if not headers_parsed:
|
||||
id_ind = row.index(id_header)
|
||||
sequence_ind = row.index(sequence_header)
|
||||
name_ind = row.index(name_header) if name_header else None
|
||||
desc_ind = row.index(desc_header) if desc_header else None
|
||||
start_ind = row.index(start_header) if start_header else None
|
||||
end_ind = row.index(end_header) if end_header else None
|
||||
sequence_ind = row.index(sequence_header)
|
||||
headers_parsed = True
|
||||
continue
|
||||
id = row[id_ind]
|
||||
sequence = row[sequence_ind]
|
||||
name = row[name_ind] if name_header else None
|
||||
desc = row[desc_ind] if desc_header else None
|
||||
start = row[start_ind] if start_header else None
|
||||
end = row[end_ind] if end_header else None
|
||||
sequence = row[sequence_ind]
|
||||
annotations[id] = AlignedSequence(
|
||||
yield QuerySequence(
|
||||
id,
|
||||
sequence,
|
||||
name,
|
||||
@ -46,18 +65,23 @@ def read_annotations_from_csv(
|
||||
int(start) if start else None,
|
||||
int(end) if end else None,
|
||||
)
|
||||
return annotations
|
||||
|
||||
|
||||
def save_alignments_to_csv(
|
||||
aligned_pairs: dict[str, tuple[AlignedSequence, AlignedSequence]], output_path: str
|
||||
):
|
||||
aligned_pairs: Iterable[tuple[QuerySequence, QuerySequence]], output_path: str
|
||||
) -> None:
|
||||
"""Saves alignments to a CSV.
|
||||
|
||||
:param aligned_pairs: An iterable of the original sequence and aligned sequences
|
||||
:type aligned_pairs: Iterable[tuple[AlignedSequence, AlignedSequence]]
|
||||
:param output_path: A path to the output directory
|
||||
:type output_path: str
|
||||
"""
|
||||
with open(output_path, "w") as output_fd:
|
||||
writer = csv.writer(output_fd)
|
||||
header_wrote = False
|
||||
header_order = None
|
||||
for id, annotations in aligned_pairs.items():
|
||||
original, aligned = annotations
|
||||
for original, aligned in aligned_pairs:
|
||||
original_vars = vars(original)
|
||||
aligned_vars = vars(aligned)
|
||||
if not header_wrote:
|
||||
51
tests/bmlsa/test_aligner.py
Normal file
51
tests/bmlsa/test_aligner.py
Normal file
@ -0,0 +1,51 @@
|
||||
import pytest
|
||||
from Bio import SeqIO
|
||||
from bmlsa.aligner import align_many_to_one_ssw
|
||||
from bmlsa.cli import DEFAULT_ALIGNMENT_PARAMETERS
|
||||
from bmlsa.datatypes import QuerySequence
|
||||
from collections.abc import Iterable
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
def reference_sequence():
|
||||
return str(
|
||||
list(SeqIO.parse("tests/resources/NC_045512_coding.fasta", "fasta"))[0].seq
|
||||
)
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
def queries():
|
||||
return [
|
||||
QuerySequence(
|
||||
"ORF10",
|
||||
"ATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAAT"
|
||||
"GAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAG",
|
||||
start=29558,
|
||||
end=29674,
|
||||
)
|
||||
]
|
||||
|
||||
|
||||
def test_align_many_to_one_returns_data(reference_sequence, queries):
|
||||
results = align_many_to_one_ssw(
|
||||
reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
|
||||
)
|
||||
assert isinstance(results, Iterable)
|
||||
|
||||
|
||||
def test_align_many_to_one_returns_correct_data_structure(reference_sequence, queries):
|
||||
results = align_many_to_one_ssw(
|
||||
reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
|
||||
)
|
||||
for original, aligned_seq in results:
|
||||
assert isinstance(original, QuerySequence)
|
||||
assert isinstance(aligned_seq, QuerySequence)
|
||||
|
||||
|
||||
def test_align_many_to_one_returns_correct_data(reference_sequence, queries):
|
||||
results = align_many_to_one_ssw(
|
||||
reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
|
||||
)
|
||||
for original, aligned_seq in results:
|
||||
assert original.start == aligned_seq.start
|
||||
assert original.end == aligned_seq.end
|
||||
31
tests/bmlsa/test_io.py
Normal file
31
tests/bmlsa/test_io.py
Normal file
@ -0,0 +1,31 @@
|
||||
from csv import reader
|
||||
from os import path
|
||||
from bmlsa.datatypes import QuerySequence
|
||||
from bmlsa.io import queries_from_csv, save_alignments_to_csv
|
||||
from collections.abc import Iterable
|
||||
|
||||
|
||||
def test_queries_from_csv_has_data():
|
||||
results = queries_from_csv("tests/resources/SARS_CoV-2_genes.csv", "id", "sequence")
|
||||
assert isinstance(results, Iterable)
|
||||
|
||||
|
||||
def test_queries_from_csv_data_valid():
|
||||
results = queries_from_csv("tests/resources/SARS_CoV-2_genes.csv", "id", "sequence")
|
||||
for aligned_seq in results:
|
||||
assert isinstance(aligned_seq.id, str)
|
||||
assert isinstance(aligned_seq.sequence, str)
|
||||
|
||||
|
||||
def test_save_alignments_to_csv_produces_correct_headers_in_csv(tmpdir):
|
||||
output_path = path.join(tmpdir, "alignment_results.csv")
|
||||
dummy_sequence = QuerySequence("DUMMY", "ATACTGGAAAA", name="test_sequence")
|
||||
alignments = [(dummy_sequence, dummy_sequence)]
|
||||
save_alignments_to_csv(alignments, output_path)
|
||||
|
||||
with open(output_path, "r") as csv_fd:
|
||||
results = list(reader(csv_fd))
|
||||
vars_to_check = list(vars(dummy_sequence).keys())
|
||||
for var_to_check in vars_to_check:
|
||||
assert "original" + var_to_check in results[0]
|
||||
assert "aligned" + var_to_check in results[0]
|
||||
430
tests/resources/NC_045512_coding.fasta
Normal file
430
tests/resources/NC_045512_coding.fasta
Normal file
@ -0,0 +1,430 @@
|
||||
>NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
|
||||
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA
|
||||
CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC
|
||||
TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG
|
||||
TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC
|
||||
CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC
|
||||
GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG
|
||||
CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT
|
||||
GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC
|
||||
GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT
|
||||
TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA
|
||||
GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG
|
||||
TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG
|
||||
CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG
|
||||
TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG
|
||||
CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA
|
||||
ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA
|
||||
CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC
|
||||
CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA
|
||||
GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT
|
||||
ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG
|
||||
GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG
|
||||
CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA
|
||||
CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA
|
||||
ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA
|
||||
GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT
|
||||
TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG
|
||||
GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG
|
||||
TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC
|
||||
GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG
|
||||
ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG
|
||||
GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT
|
||||
AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA
|
||||
TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT
|
||||
AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA
|
||||
GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC
|
||||
TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT
|
||||
AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA
|
||||
GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT
|
||||
ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA
|
||||
GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT
|
||||
GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA
|
||||
ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC
|
||||
ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA
|
||||
TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG
|
||||
AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT
|
||||
TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA
|
||||
CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC
|
||||
AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT
|
||||
AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA
|
||||
GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA
|
||||
CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG
|
||||
TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT
|
||||
GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT
|
||||
TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA
|
||||
TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT
|
||||
GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA
|
||||
AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC
|
||||
TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA
|
||||
GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG
|
||||
ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT
|
||||
GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT
|
||||
GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA
|
||||
TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC
|
||||
AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA
|
||||
TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA
|
||||
CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA
|
||||
TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT
|
||||
TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG
|
||||
AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA
|
||||
ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC
|
||||
CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA
|
||||
AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA
|
||||
ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT
|
||||
AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG
|
||||
ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA
|
||||
TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA
|
||||
ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA
|
||||
ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT
|
||||
GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT
|
||||
GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT
|
||||
TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC
|
||||
ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT
|
||||
GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG
|
||||
ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG
|
||||
TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG
|
||||
TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC
|
||||
CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA
|
||||
CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT
|
||||
GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC
|
||||
CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG
|
||||
TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA
|
||||
ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA
|
||||
AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA
|
||||
TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT
|
||||
ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG
|
||||
CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC
|
||||
AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA
|
||||
TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG
|
||||
CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA
|
||||
TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC
|
||||
TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG
|
||||
GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT
|
||||
TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA
|
||||
TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT
|
||||
ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC
|
||||
TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC
|
||||
TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT
|
||||
GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG
|
||||
GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT
|
||||
GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA
|
||||
GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA
|
||||
TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC
|
||||
AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT
|
||||
GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT
|
||||
AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT
|
||||
AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG
|
||||
AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT
|
||||
TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT
|
||||
ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG
|
||||
GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT
|
||||
ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG
|
||||
AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG
|
||||
CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT
|
||||
TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA
|
||||
ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA
|
||||
ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC
|
||||
ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC
|
||||
ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC
|
||||
CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT
|
||||
TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT
|
||||
GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC
|
||||
TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC
|
||||
AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA
|
||||
GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG
|
||||
GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA
|
||||
CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC
|
||||
CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT
|
||||
ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT
|
||||
CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG
|
||||
TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG
|
||||
CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC
|
||||
GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC
|
||||
TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC
|
||||
TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC
|
||||
ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT
|
||||
GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG
|
||||
ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG
|
||||
ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG
|
||||
TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT
|
||||
ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG
|
||||
TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT
|
||||
GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA
|
||||
CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT
|
||||
TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA
|
||||
ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG
|
||||
CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA
|
||||
TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA
|
||||
ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC
|
||||
AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC
|
||||
TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC
|
||||
ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA
|
||||
TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT
|
||||
AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG
|
||||
ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT
|
||||
CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG
|
||||
TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC
|
||||
TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG
|
||||
GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA
|
||||
GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA
|
||||
GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC
|
||||
TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA
|
||||
AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA
|
||||
GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA
|
||||
GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA
|
||||
TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA
|
||||
GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG
|
||||
AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA
|
||||
TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA
|
||||
ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT
|
||||
TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG
|
||||
TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT
|
||||
GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA
|
||||
CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT
|
||||
TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC
|
||||
TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT
|
||||
ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT
|
||||
ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT
|
||||
GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT
|
||||
GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG
|
||||
TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA
|
||||
AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG
|
||||
TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA
|
||||
GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA
|
||||
CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA
|
||||
ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT
|
||||
GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC
|
||||
CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA
|
||||
ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC
|
||||
ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG
|
||||
ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT
|
||||
AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA
|
||||
GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG
|
||||
TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT
|
||||
TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA
|
||||
AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG
|
||||
ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG
|
||||
ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG
|
||||
CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT
|
||||
ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC
|
||||
AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT
|
||||
GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC
|
||||
AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG
|
||||
ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT
|
||||
AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC
|
||||
TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC
|
||||
TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC
|
||||
TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG
|
||||
GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG
|
||||
TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT
|
||||
AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA
|
||||
GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC
|
||||
AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC
|
||||
ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC
|
||||
AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC
|
||||
ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT
|
||||
GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA
|
||||
TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC
|
||||
AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC
|
||||
GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA
|
||||
TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA
|
||||
CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT
|
||||
AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG
|
||||
TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT
|
||||
ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT
|
||||
GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT
|
||||
GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA
|
||||
TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT
|
||||
GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG
|
||||
AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT
|
||||
TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT
|
||||
AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC
|
||||
GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT
|
||||
AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC
|
||||
TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG
|
||||
GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT
|
||||
GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT
|
||||
AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT
|
||||
TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA
|
||||
AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC
|
||||
ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT
|
||||
TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC
|
||||
TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA
|
||||
GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC
|
||||
AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA
|
||||
TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC
|
||||
TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA
|
||||
ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT
|
||||
GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC
|
||||
TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA
|
||||
CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT
|
||||
CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA
|
||||
GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG
|
||||
TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA
|
||||
TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA
|
||||
CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA
|
||||
GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC
|
||||
TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT
|
||||
TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA
|
||||
TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA
|
||||
TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT
|
||||
AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA
|
||||
AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA
|
||||
CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT
|
||||
GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG
|
||||
TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG
|
||||
AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC
|
||||
ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC
|
||||
CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT
|
||||
AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT
|
||||
TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA
|
||||
ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG
|
||||
ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA
|
||||
GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA
|
||||
AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA
|
||||
CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA
|
||||
CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT
|
||||
TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC
|
||||
CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG
|
||||
AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA
|
||||
AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT
|
||||
AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA
|
||||
CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA
|
||||
CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT
|
||||
ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG
|
||||
ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA
|
||||
AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT
|
||||
ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC
|
||||
GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA
|
||||
TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC
|
||||
GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT
|
||||
TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA
|
||||
ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT
|
||||
AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG
|
||||
GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG
|
||||
GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG
|
||||
GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA
|
||||
AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG
|
||||
GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA
|
||||
CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA
|
||||
ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA
|
||||
GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG
|
||||
TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC
|
||||
TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC
|
||||
CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT
|
||||
TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC
|
||||
GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC
|
||||
AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA
|
||||
TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT
|
||||
TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA
|
||||
GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA
|
||||
ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT
|
||||
GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT
|
||||
GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG
|
||||
TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC
|
||||
ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT
|
||||
GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG
|
||||
ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC
|
||||
TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA
|
||||
GATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACT
|
||||
TTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACT
|
||||
TTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAAC
|
||||
AAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTC
|
||||
TGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGA
|
||||
GATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAAC
|
||||
CAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTA
|
||||
CTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGC
|
||||
TGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT
|
||||
CAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTG
|
||||
GTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTAC
|
||||
CACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCA
|
||||
ACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAA
|
||||
TAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACC
|
||||
AATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCA
|
||||
TTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATT
|
||||
GCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACC
|
||||
TTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGG
|
||||
ACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTG
|
||||
GAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAA
|
||||
AATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCA
|
||||
CAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATA
|
||||
TCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAG
|
||||
TTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCT
|
||||
ACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTA
|
||||
TGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAA
|
||||
GAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTT
|
||||
TCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACA
|
||||
CATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACC
|
||||
TGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTA
|
||||
GGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTG
|
||||
CCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCC
|
||||
ATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGT
|
||||
ATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACG
|
||||
ACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGA
|
||||
ATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTC
|
||||
GCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCT
|
||||
TGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGT
|
||||
GTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTG
|
||||
GCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAAT
|
||||
AATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTT
|
||||
CTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTA
|
||||
CTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATG
|
||||
GGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCA
|
||||
ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC
|
||||
CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT
|
||||
TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC
|
||||
TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT
|
||||
TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT
|
||||
GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT
|
||||
CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA
|
||||
TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC
|
||||
CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA
|
||||
AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT
|
||||
AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC
|
||||
ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC
|
||||
TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT
|
||||
GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA
|
||||
GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG
|
||||
ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG
|
||||
CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC
|
||||
TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA
|
||||
AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC
|
||||
CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA
|
||||
GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA
|
||||
TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT
|
||||
TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT
|
||||
GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT
|
||||
ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG
|
||||
CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA
|
||||
GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG
|
||||
TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC
|
||||
GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA
|
||||
TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT
|
||||
GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA
|
||||
AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG
|
||||
ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG
|
||||
TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT
|
||||
GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC
|
||||
CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG
|
||||
TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT
|
||||
GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA
|
||||
AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC
|
||||
ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT
|
||||
AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA
|
||||
ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG
|
||||
TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG
|
||||
CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC
|
||||
AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA
|
||||
ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG
|
||||
TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC
|
||||
TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC
|
||||
TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT
|
||||
TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG
|
||||
CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT
|
||||
GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT
|
||||
TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC
|
||||
GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT
|
||||
TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA
|
||||
AAAAAAAAAAAAA
|
||||
|
||||
8
tests/resources/SARS_CoV-2_genes.csv
Normal file
8
tests/resources/SARS_CoV-2_genes.csv
Normal file
@ -0,0 +1,8 @@
|
||||
id,sequence,start,end
|
||||
ORF8,"ATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGT
|
||||
CATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATAT
|
||||
TAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCC
|
||||
ATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTA
|
||||
AATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGT
|
||||
ATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAA",27894,28259
|
||||
ORF10,ATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAG,29558,29674
|
||||
|
Loading…
Reference in New Issue
Block a user