diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 45f664e14..b1fd84e83 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -41,19 +41,18 @@ jobs: strategy: matrix: python-version: - - '3.8' - '3.9' - '3.10' - '3.11' - '3.12' - biopython-version: - # list of Biopython versions with support for a new Python version - # from https://github.com/biopython/biopython/blob/master/NEWS.rst + biopython-version: + # list of Biopython versions with support for a new Python version + # from https://github.com/biopython/biopython/blob/master/NEWS.rst - '1.80' # first to support Python 3.10 and 3.11 - '1.82' # first to support Python 3.12 - - '' # latest - exclude: - # some older Biopython versions are incompatible with later Python versions + - '' # latest + exclude: + # some older Biopython versions are incompatible with later Python versions - { biopython-version: '1.80', python-version: '3.12' } defaults: run: @@ -115,7 +114,11 @@ jobs: - lassa - measles - mpox + - oropouche + - rabies - seasonal-cov + - wnv + - yellow-fever - zika name: pathogen-repo-ci (${{ matrix.pathogen }}) diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index c99890fee..27a914224 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -10,7 +10,7 @@ on: type: string jobs: run: - if: github.ref == github.event.repository.default_branch + if: github.ref_name == github.event.repository.default_branch uses: ./.github/workflows/ci.yaml secrets: inherit with: diff --git a/.pylintrc b/.pylintrc index 023aa51ed..07a082fff 100644 --- a/.pylintrc +++ b/.pylintrc @@ -317,13 +317,6 @@ max-line-length=100 # Maximum number of lines in a module max-module-lines=1000 -# List of optional constructs for which whitespace checking is disabled. `dict- -# separator` is used to allow tabulation in dicts, etc.: {1 : 1,\n222: 2}. -# `trailing-comma` allows a space between comma and closing bracket: (a, ). -# `empty-line` allows space-only lines. -no-space-check=trailing-comma, - dict-separator - # Allow the body of a class to be on the same line as the declaration if body # contains single statement. single-line-class-stmt=no diff --git a/.readthedocs.yml b/.readthedocs.yml index e958dd6de..791a83096 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -11,6 +11,9 @@ build: # generated from the full git history in conf.py. - git fetch --unshallow +sphinx: + configuration: docs/conf.py + python: install: - method: pip diff --git a/CHANGES.md b/CHANGES.md index 0cbbae210..9d209f767 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -9,9 +9,28 @@ ### Bug Fixes * ancestral, refine: Explicitly specify how the root and ambiguous states are handled during sequence reconstruction and mutation counting. [#1690][] (@rneher) +* titers: Fix type errors in code associated with cross-validation of models. [#1688][] (@huddlej) +[#1688]: https://github.com/nextstrain/augur/pull/1688 [#1690]: https://github.com/nextstrain/augur/pull/1690 +## 27.0.0 (9 December 2024) + +### Major Changes + +- Drop support for Python 3.8. [#1693] (@victorlin) +- Drop support for older versions of jsonschema (<4.18.0). [#1691] (@victorlin) +- Drop support for xopen <2.0.0. [#1692] (@victorlin) + +### Bug fixes + +- export: validation will no longer crash with `KeyError: 'tree'` when newer versions of jsonschema (≥4.18.0) are installed. [#1358] (@victorlin) + +[#1358]: https://github.com/nextstrain/augur/issues/1358 +[#1691]: https://github.com/nextstrain/augur/pull/1691 +[#1692]: https://github.com/nextstrain/augur/pull/1692 +[#1693]: https://github.com/nextstrain/augur/pull/1693 + ## 26.2.0 (20 November 2024) ### Features diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 000000000..c8328c8fc --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,45 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite it as below." + +preferred-citation: + type: article + title: "Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens" + doi: "10.21105/joss.02906" + journal: "Journal of Open Source Software" + year: 2021 + month: 1 + volume: 6 + issue: 57 + start: 2906 + end: 2906 + + authors: + - family-names: Huddleston + given-names: John + + - family-names: Hadfield + given-names: James + + - family-names: Sibley + given-names: Thomas R. + + - family-names: Lee + given-names: Jover + + - family-names: Fay + given-names: Kairsten + + - family-names: Ilcisin + given-names: Misja + + - family-names: Harkins + given-names: Elias + + - family-names: Bedford + given-names: Trevor + + - family-names: Neher + given-names: Richard A. + + - family-names: Hodcroft + given-names: Emma B. diff --git a/DEPRECATED.md b/DEPRECATED.md index 4523d354f..667bded3a 100644 --- a/DEPRECATED.md +++ b/DEPRECATED.md @@ -6,7 +6,7 @@ available for backwards compatibility, but should not be used in new code. ## `xopen` major version 1 -*Deprecated in version 25.1.0 (July 2024). Planned for removal November 2024 or after.* +*Deprecated in version 25.1.0 (July 2024). Removed in version 27.0.0 (December 2024).* ## `augur parse` preference of `name` over `strain` as the sequence ID field diff --git a/README.md b/README.md index cac384427..64a8fd508 100644 --- a/README.md +++ b/README.md @@ -40,6 +40,8 @@ Try out an analysis of real virus data by [completing the Zika tutorial](https:/ Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB, (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), 2906, https://doi.org/10.21105/joss.02906 +For other formats, refer to [CITATION.cff](./CITATION.cff). + ## License and copyright Copyright 2014-2022 Trevor Bedford and Richard Neher. diff --git a/augur/__main__.py b/augur/__main__.py index 59f89dd8f..68b3a0bde 100644 --- a/augur/__main__.py +++ b/augur/__main__.py @@ -24,11 +24,7 @@ def main(): errors="backslashreplace", newline=None, - # Always line-buffer stderr since we only use it for messaging, not - # data output. This is the Python default from 3.9 onwards, but we - # also run on 3.8 where it's not. Be consistent regardless of Python - # version. - line_buffering=True, + # By default, stderr is always line-buffered. ) return augur.run( argv[1:] ) diff --git a/augur/__version__.py b/augur/__version__.py index 3f47307d8..9b9c5d5d6 100644 --- a/augur/__version__.py +++ b/augur/__version__.py @@ -1,4 +1,4 @@ -__version__ = '26.2.0' +__version__ = '27.0.0' def is_augur_version_compatible(version): diff --git a/augur/io/file.py b/augur/io/file.py index 1aa5f59af..2b9883f32 100644 --- a/augur/io/file.py +++ b/augur/io/file.py @@ -2,21 +2,9 @@ from contextlib import contextmanager from io import IOBase from textwrap import dedent -from xopen import xopen +from xopen import xopen, _PipedCompressionProgram from augur.errors import AugurError -# Workaround to maintain compatibility with both xopen v1 and v2 -# Around November 2024, we shall drop support for xopen v1 -# by removing the try-except block and using -# _PipedCompressionProgram directly -try: - from xopen import _PipedCompressionProgram as PipedCompressionReader - from xopen import _PipedCompressionProgram as PipedCompressionWriter -except ImportError: - from xopen import ( # type: ignore[attr-defined, no-redef] - PipedCompressionReader, - PipedCompressionWriter, - ) ENCODING = "utf-8" @@ -63,7 +51,7 @@ def open_file(path_or_buffer, mode="r", **kwargs): Try re-saving the file using the {e.encoding!r} encoding.""")) - elif isinstance(path_or_buffer, (IOBase, PipedCompressionReader, PipedCompressionWriter)): + elif isinstance(path_or_buffer, (IOBase, _PipedCompressionProgram)): yield path_or_buffer else: diff --git a/augur/titer_model.py b/augur/titer_model.py index 92b213be0..0112f49f1 100644 --- a/augur/titer_model.py +++ b/augur/titer_model.py @@ -38,42 +38,42 @@ def load_from_file(filenames, excluded_sources=None): >>> type(measurements) >>> len(measurements) - 11 + 248 >>> len(strains) - 13 + 62 >>> len(sources) - 5 + 15 Inspect specific measurements. First, inspect a measurement that has a specific value in the input. - >>> measurements[("A/Acores/11/2013", ("A/Alabama/5/2010", "F27/10"))] - [80.0] + >>> measurements[("A/Wisconsin/3/2007", ("A/Wisconsin/3/2007", "A/Wis3/07"))] + [5120.0] Next, inspect a measurement that has a thresholded value at the lower - bound of detection (e.g., "<80"). This measurement should be reported as - one half of its threshold value (e.g., 40.0). + bound of detection (e.g., "<40"). This measurement should be reported as + one half of its threshold value (e.g., 20.0). - >>> measurements[("A/Acores/11/2013", ("A/Victoria/208/2009", "F7/10"))] - [40.0] + >>> measurements[("A/HongKong/1/1968", ("A/Victoria/3/1975", "A/Vic/3/75"))] + [20.0] Inspect a measurement that has a thresholded value at the upper bound of - detection (">1280"). This measurement should be reported as twice its - threshold value (e.g., 2560.0). + detection (">5120"). This measurement should be reported as twice its + threshold value (e.g., 10240.0). - >>> measurements[("A/Acores/SU43/2012", ("A/Texas/50/2012", "F36/12"))] - [2560.0] + >>> measurements[("A/Wisconsin/3/2007", ("A/Uruguay/716/2007", "A/Uru716/07"))] + [10240.0] Confirm that excluding sources produces fewer measurements. - >>> measurements, strains, sources = TiterCollection.load_from_file("tests/data/titer_model/h3n2_titers_subset.tsv", excluded_sources=["NIMR_Sep2013_7-11.csv"]) + >>> measurements, strains, sources = TiterCollection.load_from_file("tests/data/titer_model/h3n2_titers_subset.tsv", excluded_sources=["Hay2001"]) >>> len(measurements) - 5 + 223 Request measurements for a test/reference/serum tuple that should not exist after excluding its source. - >>> measurements.get(("A/Acores/11/2013", ("A/Alabama/5/2010", "F27/10"))) + >>> measurements.get(("A/HongKong/1/1968", ("A/HongKong/1/1968", "A/HK/1/68"))) >>> Missing titer data should produce an error. @@ -150,12 +150,10 @@ def count_strains(titers): -------- >>> measurements, strains, sources = TiterCollection.load_from_file("tests/data/titer_model/h3n2_titers_subset.tsv") >>> titer_counts = TiterCollection.count_strains(measurements) - >>> titer_counts["A/Acores/11/2013"] - 6 - >>> titer_counts["A/Acores/SU43/2012"] - 3 - >>> titer_counts["A/Cairo/63/2012"] - 2 + >>> titer_counts["A/Auckland/6/2003"] + 4 + >>> titer_counts["A/Brisbane/9/2006"] + 15 """ counts = defaultdict(int) for key in titers.keys(): @@ -187,22 +185,26 @@ def filter_strains(titers, strains): -------- >>> measurements, strains, sources = TiterCollection.load_from_file("tests/data/titer_model/h3n2_titers_subset.tsv") >>> len(measurements) - 11 + 248 Test the case when a test strain exists in the subset but the none of its corresponding reference strains do. - >>> len(TiterCollection.filter_strains(measurements, ["A/Acores/11/2013"])) + >>> len(TiterCollection.filter_strains(measurements, ["A/Oslo/244/1997"])) 0 - Test when both the test and reference strains exist in the subset. + Test when both the test and reference strains exist in the subset. This + first test gets a heterologous pair (first and second strain) and the + autologous pair for the second strain. - >>> len(TiterCollection.filter_strains(measurements, ["A/Acores/11/2013", "A/Alabama/5/2010", "A/Athens/112/2012"])) + >>> len(TiterCollection.filter_strains(measurements, ["A/Oslo/244/1997", "A/Johannesburg/33/1994"])) 2 - >>> len(TiterCollection.filter_strains(measurements, ["A/Acores/11/2013", "A/Acores/SU43/2012", "A/Alabama/5/2010", "A/Athens/112/2012"])) - 3 + + Test when no strains are provided. + >>> len(TiterCollection.filter_strains(measurements, [])) 0 + """ return {key: value for key, value in titers.items() if key[0] in strains and key[1][0] in strains} @@ -226,7 +228,7 @@ def __init__(self, titers, **kwargs): else: self.titers = titers strain_counts = type(self).count_strains(titers) - self.strains = strain_counts.keys() + self.strains = list(strain_counts.keys()) def read_titers(self, fname): self.titer_fname = fname @@ -318,11 +320,11 @@ def strain_census(self, titers): >>> titers = TiterCollection(measurements) >>> sera, ref_strains, test_strains = titers.strain_census(measurements) >>> len(sera) - 9 + 66 >>> len(ref_strains) - 9 + 27 >>> len(test_strains) - 13 + 62 Parameters ---------- @@ -415,7 +417,7 @@ def make_training_set(self, training_fraction=1.0, subset_strains=False, **kwarg from random import sample tmp = set(self.test_strains) tmp.difference_update(self.ref_strains) # don't use references viruses in the set to sample from - training_strains = sample(tmp, int(training_fraction*len(tmp))) + training_strains = sample(sorted(tmp), int(training_fraction*len(tmp))) for tmpstrain in self.ref_strains: # add all reference viruses to the training set if tmpstrain not in training_strains: training_strains.append(tmpstrain) @@ -504,7 +506,7 @@ def validate(self, plot=False, cutoff=0.0, validation_set = None, fname=None): pred_titer = self.predict_titer(key[0], key[1], cutoff=cutoff) validation[key] = (val, pred_titer) - validation_array = np.array(validation.values()) + validation_array = np.array(list(validation.values())) actual = validation_array[:,0] predicted = validation_array[:,1] @@ -517,7 +519,7 @@ def validate(self, plot=False, cutoff=0.0, validation_set = None, fname=None): 'rms_error': np.sqrt(np.mean((actual-predicted)**2)), } pprint(model_performance) - model_performance['values'] = validation.values() + model_performance['values'] = list(validation.values()) self.validation = model_performance diff --git a/augur/util_support/node_data.py b/augur/util_support/node_data.py index 62b553663..0bb77bdf9 100644 --- a/augur/util_support/node_data.py +++ b/augur/util_support/node_data.py @@ -31,8 +31,6 @@ def deep_add_or_update(self, d, key, value): raise exception """ - # TODO Python 3.9: Use the new dictionary union operator (https://www.python.org/dev/peps/pep-0584/) - if key not in d or ( not isinstance(d[key], dict) and not isinstance(value, dict) ): diff --git a/augur/validate.py b/augur/validate.py index 364a5d785..da758f2b5 100644 --- a/augur/validate.py +++ b/augur/validate.py @@ -9,6 +9,7 @@ import jsonschema.exceptions import re from itertools import groupby +from referencing import Registry from textwrap import indent from typing import Iterable, Union from augur.data import as_file @@ -48,22 +49,24 @@ def load_json_schema(path, refs=None): for k, v in refs.items(): with as_file(v) as file, open_file(file, "r") as fh: schema_store[k] = json.load(fh) - resolver = jsonschema.RefResolver.from_schema(schema,store=schema_store) - schema_validator = Validator(schema, resolver=resolver) + + # Create a dummy retrieval function to handle URIs not present in + # schema_store. This often indicates a typo (the $ref doesn't match the + # key of the schema_store) or we forgot to add a local mapping for a new + # $ref. + def retrieve(uri): + # Take advantage of the fact that BaseException is not handled by + # Registry.get_or_retrieve. This means the custom error message is + # printed instead of the less helpful default: + # jsonschema.exceptions._WrappedReferencingError: Unresolvable: https://… + raise BaseException(f"The schema used for validation could not resolve a local file for {uri!r}. " + + "Please check the schema used and update the appropriate schema_store as needed." ) + + registry = Registry(retrieve=retrieve).with_contents(schema_store.items()) + schema_validator = Validator(schema, registry=registry) else: schema_validator = Validator(schema) - # By default $ref URLs which we don't define in a schema_store are fetched - # by jsonschema. This often indicates a typo (the $ref doesn't match the key - # of the schema_store) or we forgot to add a local mapping for a new $ref. - # Either way, Augur should not be accessing the network. - def resolve_remote(url): - # The exception type is not important as jsonschema will catch & re-raise as a RefResolutionError - raise Exception(f"The schema used for validation attempted to fetch the remote URL {url!r}. " + - "Augur should resolve schema references to local files, please check the schema used " + - "and update the appropriate schema_store as needed." ) - schema_validator.resolver.resolve_remote = resolve_remote - return schema_validator diff --git a/docs/conf.py b/docs/conf.py index 9fa3145d2..7b439c465 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -157,9 +157,10 @@ def prose_list(items): ## string" matching happening, and something like a plain `r'google'` ## regular expression will _NOT_ match all google.com URLs. linkcheck_ignore = [ - # This URL will occasionally fail and return 403 (broken). + # These URLs will occasionally fail and return 403 (broken). # r'^http://www\.microbesonline\.org/fasttree/', + r'^https://academic\.oup\.com/ve/article/4/1/vex042/4794731', ] linkcheck_anchors_ignore_for_url = [ # Github uses anchor-looking links for highlighting lines but diff --git a/docs/contribute/DEV_DOCS.md b/docs/contribute/DEV_DOCS.md index c46542819..1d3b89e74 100644 --- a/docs/contribute/DEV_DOCS.md +++ b/docs/contribute/DEV_DOCS.md @@ -17,7 +17,7 @@ Please see the [open issues list](https://github.com/nextstrain/augur/issues) fo ## Contributing code -We currently target compatibility with Python 3.8 and higher. As Python releases new versions, +We currently target compatibility with Python 3.9 and higher. As Python releases new versions, the minimum target compatibility may be increased in the future. ### Running local changes diff --git a/docs/installation/installation.rst b/docs/installation/installation.rst index 34f82e919..172686459 100644 --- a/docs/installation/installation.rst +++ b/docs/installation/installation.rst @@ -45,7 +45,7 @@ There are several ways to install Augur, ordered from least to most complex. .. warning:: Installing other Python packages after Augur may cause dependency incompatibilities. If this happens, re-install Augur using the command in step 1. - Augur is written in Python 3 and requires at least Python 3.8. It's published on `PyPI `__ as `nextstrain-augur `__. + Augur is written in Python 3 and requires at least Python 3.9. It's published on `PyPI `__ as `nextstrain-augur `__. 1. Install Augur along with Python dependencies. diff --git a/mypy.ini b/mypy.ini index 56de27ade..873e5c085 100644 --- a/mypy.ini +++ b/mypy.ini @@ -1,6 +1,6 @@ [mypy] # Check against lowest compatible Python version -python_version = 3.8 +python_version = 3.9 # Don't set python_version. Instead, use the default behavior of checking for # compatibility against the version of Python used to run mypy. diff --git a/pyrightconfig.json b/pyrightconfig.json index 0fbcad0c2..90c0c23fd 100644 --- a/pyrightconfig.json +++ b/pyrightconfig.json @@ -1,7 +1,7 @@ { // Check against lowest compatible Python version // Sync this with python-version in .github/workflows/ci.yaml:jobs.pyright - "pythonVersion": "3.8", + "pythonVersion": "3.9", "include": ["augur/"], diff --git a/setup.py b/setup.py index 81aad167d..a2545fe3a 100644 --- a/setup.py +++ b/setup.py @@ -57,7 +57,7 @@ "cvxopt >=1.1.9, ==1.*", "importlib_resources >=5.3.0; python_version < '3.11'", "isodate ==0.6.*", - "jsonschema >=3.0.0, ==3.*", + "jsonschema >=4.18.0, ==4.*", "networkx >= 2.5, <4", "numpy ==1.*", "packaging >=19.2", @@ -65,8 +65,9 @@ "phylo-treetime >=0.11.2, <0.12", "pyfastx >=1.0.0, <3.0", "python_calamine >=0.2.0", + "referencing >=0.29.1, <1.0", "scipy ==1.*", - "xopen[zstd] >=1.7.0, <3" # TODO: Deprecated, remove v1 support around November 2024 + "xopen[zstd] >=2.0.0, <3" ], extras_require = { 'dev': [ @@ -102,7 +103,6 @@ # Python 3 only "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", diff --git a/tests/data/titer_model/h3n2_ha_aligned_genbank_HA1.fasta b/tests/data/titer_model/h3n2_ha_aligned_genbank_HA1.fasta new file mode 100644 index 000000000..369ce3347 --- /dev/null +++ b/tests/data/titer_model/h3n2_ha_aligned_genbank_HA1.fasta @@ -0,0 +1,833 @@ +>A/Auckland/6/2003 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVVPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Bilthoven/16190/1968 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILD +GINCTLIDALLGDPHCDVFQDETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +ITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIW +GVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPG +DVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>A/Bilthoven/2271/1976 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICNNPHRILD +GINCTLIDALLGDPHCDGFQNKKWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +INEGFNWTGVTQNGGSYACKRGPDNGFFSRLNWLYKSESTYPVLNVTMPNNDNFDKLYIW +GVHHPSTDKEQTNLYVQASGRVTVSTKRSQQTIIPNVGSRPWVRGLSSRISIYWTIVKPG +DILVINSNGNLIAPRGYFKIRNGKSSIMRSDAPIGTCSSECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>A/Bilthoven/5146/1974 +QNFPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILD +GIDCTLIDALLGDPHCDGFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +INEGFTWTGVTQNGGSNACKRGPDIGFFSRLNWLYKSGNTYPVLNVSMPNNDNFDKLYIW +GVHHPSTDQEQTSLYVQASGRVTVSTKRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPG +DILVINSNGNLIAPRGYFKMRTGKSSIMRSDASIGTCISECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>A/Bilthoven/5168/1976 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICDNPHRILD +GINCTLIDALLGDPHCDGFQNEKWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +INEGFNWTGVTQNGGSSACKRGPDNGFFSRLNWLYKSGSTYPVQNVTMPNNDNSDKLYIW +GVHHPSTDKEQTDLYVQASGKVTVSTKRSQQTVIPNVGSRPWVRGLSSRVSIYWTIVKPG +DILIINSNGNLIAPRGYFKMRTGKSSIMRSDAPIGTCSSECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>A/Bilthoven/93/1970 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILD +GVNCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +ITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIW +GVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGQSSRISIYWTIVKPG +DVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>A/Brisbane/3/2005 +QKLPGNDNSTATLCIGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLIASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNNSFFSRLNWLTHLKFKYPALNVTMPNNEEFDKLYIW +GVHHPGTDNDQISLYAQASGKITVSTKRSQQTVIPNIGSRPRVRDIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Brisbane/5/2002 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPHCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Brisbane/6/2002 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPHCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Brisbane/7/2003 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFDWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Brisbane/9/2006 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNNSFFSRLNWLTQLKFKYPALNVTMPNNEKFDKLYIW +GVHHPVTDNDQIFLYAQASGRITVSTKRSQQTVIPNIGSRPRVRNIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/California/20/2005 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSSCKRRSNNSFFSRLNWLTRLKFKYPALNVTMPNNEKFDKLYIW +GVHHPVTDNDQIFLYAQASGRITVSTKRSQQTVIPNIGSRPRVRNIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Cheonnam/432/2002 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQTSLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/ChristChurch/2/1988 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNEKWDLFIERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +INEGFNWTGVTQNGGSYACKRGSVNSFFSRLNWLYESEYKYPALNVTMPNNGKFDKLYIW +GVHHPITEKEQTNLYVRASGRVTVSTKRSQQTRIPNIGSRPWVRGLSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRTGKSSIMRSDAPIGTCSSECITPNGSIPNDKPFQNVNKI +TYGACPRYGKQNTLKLATGMRNVPEKQTR +>A/England/392/2008 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGEICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLRFKYPALNVTMPNNEQFDKLYIW +GVHHPGTDNDQIFLYAQASGRITVSTKRSQQTVIPNIGSRPRVRNIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/England/394/2008 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGEICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVSDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLRFKYPALNVTMPNNEQFDKLYIW +GVHHPGTDNDQIFLYAQASGRITVSTKRSQQTVIPNIGSRPRVRNIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/England/42/1972 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILD +GIDCTLIDALLGDPHCDGFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +INEGFTWTGVTQNGGSNACKRGPDSGFFSRLNWLYKSGSTYPVLNVTMPNNDNFDKLYIW +GVHHPSTNQEQTSLYVQASGRVTVSTKGSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPG +DILVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIGTCISECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>A/Fujian/445/2003 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPVTDSDQINLYAQASGRITVSTKRSQQTVIPNIGYRPRVRDIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Geneva/AI9509/1995 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +TKEGFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGISSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/HongKong/1/1968 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILD +GIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +ITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIW +GVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIWSRPWVRGLSSRISIYWTIVKPG +DVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>A/HongKong/1550/2002 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPHCDGFQNKKWDLFVERSKAYSSCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPVTDSDQISIYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/HongKong/26560/2009 +QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGEICDSPHQILD +GKNCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACIRRSKNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIW +GVHHPGTDKDQIFPYAQASGRITVSTKRSQQTAIPNIGSRPRVRNIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSGCITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/HongKong/280/1997 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSTAYSNCYPYDVPDYASLRSLVASSGTLEF +TNEGFNWTGVAQDGTSYACKRRSVKSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVHASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIDNCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/HongKong/32/1995 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +TNEGFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGISSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/HongKong/38/1995 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +TKEGFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGISSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCKSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/HongKong/55/1994 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSPTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INENFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKRSQQTVIPDIGYRPWVRGLSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Johannesburg/33/1994 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSPTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INENFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKRSQQTVIPDIGYRPWVRGQSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Johannesburg/47/1994 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQNSPTGRICDSPHRILD +GKNCTLIDALLGDPHCDGLQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INENFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKRSQQTVIPDIGYRPWVRGQSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKLRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGPCPRYVKQNTLKLATGMRNVPEKQTR +>A/Leningrad/360/1986 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNEKWDLFIERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +INEGFNWTGVTQSGGSYTCKRGSVNSFFSRLNWLYESEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTEKEQTNLYVRASGRVTVSTKRSQQTVIPNIGSSPWVRGLSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRTGKSSIMRSDAPIGTCSSECITPNGSIPNDKPFQNVNKI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Louisiana/4/2003 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITDDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFDWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYIKQNTLKLATGMRNVPEKQTR +>A/Lyon/108/2005 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRISNNSFFSRLNWLTHLKFKYPALNVTMPNNEKFDKLYIW +GVHHPGTDNDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDIPSRISIYWTIVKPG +DILLVNSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Madrid/G130/1993 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INEDFNWTGVAQDGGSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKRSQQTVTPNIGSRPWVRGLSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDVPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Nepal/921/2006 +QKLPGIDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGEICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWAGVTQNGTSSACKRGSNNSFFSRLNWLTHSKFKYPALNVTMPNNEEFDKLYIW +GVLHPGTDNDQIFLYAQASGRITVSTKRSQQTVIPNIGSRPRVRNIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Netherlands/115/1993 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INEDFNWTGVAQDGGSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKISQQTVIPNIGSRPWVRGLSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Netherlands/371/1993 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INEDFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVATKRSQQTVIPNIGFRPWVRGQSSGISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/Netherlands/414/1998 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVQDYASLRSLVASSGTLEF +NNESFNWTGVAQNGTSYACKRRSIKSFFSRLNWLHQLKYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG 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+TNEGFNWTGVAQDGTSYACKRGSVKSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIDNCNSECITPNGSIPNDKPFQNVNRI +TYGPCPRYVKQNTLKLATGMRNVPEKQTR +>A/Philippines/1159050/2002 +QKLPGNDNSTATLCLGHHAVSNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILD +GENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRGSNKSFFSRLNWLHQLKDKYPALNVTMPNNEKFDKLYIW +GVLHPSTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>A/RhodeIsland/1/2010 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSAGEICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSRAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIW +GVLHPGTYKDQIFLYAQASGRITVSTKRSQQAVIPNIGSRPRVRNIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQSTLKLATGMRNVPEKQTR +>A/Seoul/1/1990 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+DILVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIGTCSSECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>NODE_0000012 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILD +GINCTLIDALLGDPHCDGFQNEKWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +INEGFNWTGVTQNGGSSACKRGPDSGFFSRLNWLYKSGSTYPVQNVTMPNNDNSDKLYIW +GVHHPSTDKEQTNLYVQASGKVTVSTKRSQQTIIPNVGSRPWVRGLSSRISIYWTIVKPG +DILVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIGTCSSECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>NODE_0000013 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILD +GIDCTLIDALLGDPHCDGFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +INEGFTWTGVTQNGGSNACKRGPDSGFFSRLNWLYKSGSTYPVLNVTMPNNDNFDKLYIW +GVHHPSTDQEQTSLYVQASGRVTVSTKRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPG +DILVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIGTCISECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>NODE_0000014 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILD +GIDCTLIDALLGDPHCDGFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +INEGFTWTGVTQNGGSNACKRGPDSGFFSRLNWLYKSGSTYPVLNVTMPNNDNFDKLYIW +GVHHPSTNQEQTSLYVQASGRVTVSTKRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPG +DILVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIGTCISECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>NODE_0000015 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILD +GINCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +ITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIW +GVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPG +DVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>NODE_0000016 +QDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILD +GINCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEF +ITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIW +GVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPG +DVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKI +TYGACPKYVKQNTLKLATGMRNVPEKQTR +>NODE_0000017 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INEDFNWTGVAQDGGSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKRSQQTVIPNIGSRPWVRGLSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000018 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INEDFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKRSQQTVIPNIGSRPWVRGLSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000019 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INEDFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKRSQQTVIPNIGSRPWVRGQSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000020 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSPTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INENFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKRSQQTVIPDIGYRPWVRGQSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000021 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSPTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +INENFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNGKFDKLYIW +GVHHPSTDSDQTSLYVRASGRVTVSTKRSQQTVIPDIGYRPWVRGQSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCSSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000022 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +TNEGFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGISSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000023 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +TKEGFNWTGVAQDGKSYACKRGSVNSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGISSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGNCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000024 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +TNEGFNWTGVAQDGTSYACKRGSVKSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGISSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGNCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000025 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +TNEGFNWTGVAQDGTSYACKRGSVKSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGNCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000026 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GKNCTLIDALLGDPHCDGFQNKEWDLFVERSTAYSNCYPYDVPDYASLRSLVASSGTLEF +TNEGFNWTGVAQDGTSYACKRGSVKSFFSRLNWLHKLEYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYVQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIDNCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000027 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHRILD +GENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVAQNGTSYACKRRSIKSFFSRLNWLHQLKYKYPALNVTMPNNDKFDKLYIW +GVHHPSTDSDQTSLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000028 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILD +GENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPSTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000029 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILD +GENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000030 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILD +GENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYVSLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000031 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILD +GENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYVSLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRRSDKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000032 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILD +GENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYVSLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRRSDKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000033 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPHCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000034 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPHCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000035 +QKLPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPHCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNKSFFSRLNWLHQLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000036 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000037 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000038 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFDWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000039 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFDWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDVSSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000040 +QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF +NNESFNWTGVTQNGTSSACKRRSNKSFFSRLNWLTHLKYKYPALNVTMPNNEKFDKLYIW +GVHHPGTDSDQISLYAQASGRITVSTKRSQQTVIPNIGSRPRVRDIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQNTLKLATGMRNVPEKQTR +>NODE_0000041 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A/Wisconsin/15/2009 A/Wis/15/09_F24/09 nimr-sep-2011-2011-06-24 160 +A/Wisconsin/15/2009 A/Wisconsin/15/2009 A/Wis/15/09_F24/09 nimr-sep-2011-2011-06-24b 160 diff --git a/tests/test_titer_models.py b/tests/test_titer_models.py index b0ac53ddc..16351b31a 100644 --- a/tests/test_titer_models.py +++ b/tests/test_titer_models.py @@ -1,5 +1,6 @@ - -from augur.titer_model import TiterCollection +from augur.reconstruct_sequences import load_alignments +from augur.titer_model import TiterCollection, TreeModel, SubstitutionModel +from augur.utils import read_tree def test_titer_collection(): @@ -7,4 +8,64 @@ def test_titer_collection(): titers = TiterCollection("tests/data/titer_model/h3n2_titers_subset.tsv") # Confirm that all distinct test and reference strains have been counted. - assert len(titers.strains) == 13 + assert len(titers.strains) == 62 + + +def test_titer_tree_model_validate_measurements(): + """Validate titer tree model with a subset of measurements. + """ + # Load tree. + tree = read_tree("tests/data/titer_model/h3n2_ha_tree.nwk") + + # Prepare model. + model = TreeModel(tree, "tests/data/titer_model/h3n2_titers_subset.tsv") + model.prepare( + training_fraction=0.8, + subset_strains=False, + ) + + # Train the model. + model.train() + + # Validate model on a subset of measurements. + performance = model.validate() + + +def test_titer_tree_model_validate_strains(): + """Validate titer tree model with a subset of virus strains. + """ + # Load tree. + tree = read_tree("tests/data/titer_model/h3n2_ha_tree.nwk") + + # Prepare model. + model = TreeModel(tree, "tests/data/titer_model/h3n2_titers_subset.tsv") + model.prepare( + training_fraction=0.8, + subset_strains=True, + ) + + # Train the model. + model.train() + + # Validate model on a subset of measurements. + performance = model.validate() + + +def test_titer_substitution_model_validate_measurements(): + """Validate titer substitution model with a subset of measurements. + """ + # Load alignments. + alignments = load_alignments(["tests/data/titer_model/h3n2_ha_aligned_genbank_HA1.fasta"], ["HA1"]) + + # Prepare model. + model = SubstitutionModel(alignments, "tests/data/titer_model/h3n2_titers_subset.tsv") + model.prepare( + training_fraction=0.8, + subset_strains=False, + ) + + # Train the model. + model.train() + + # Validate model on a subset of measurements. + performance = model.validate()