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test_tax_utils.py
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test_tax_utils.py
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"""
Tests for functions in taxonomy submodule.
"""
import pytest
from pytest import approx
import os
from os.path import basename
import gzip
import sourmash_tst_utils as utils
from sourmash.tax.tax_utils import (ascending_taxlist, get_ident, load_gather_results,
collect_gather_csvs, check_and_load_gather_csvs,
SummarizedGatherResult, ClassificationResult,
QueryInfo, GatherRow, TaxResult, QueryTaxResult,
BaseLineageInfo, RankLineageInfo, LineagePair,
aggregate_by_lineage_at_rank, format_for_krona,
write_krona, write_lineage_sample_frac,
LineageDB, LineageDB_Sqlite, MultiLineageDB)
# import lca utils as needed
from sourmash.lca import lca_utils
# utility functions for testing
def make_mini_taxonomy(tax_info):
#pass in list of tuples: (name, lineage)
taxD = {}
for (name,lin) in tax_info:
taxD[name] = lca_utils.make_lineage(lin)
return taxD
def make_GatherRow(gather_dict=None, exclude_cols=[]):
"""Load artificial gather row (dict) into GatherRow class"""
# default contains just the essential cols
gatherD = {'query_name': 'q1',
'query_md5': 'md5',
'query_filename': 'query_fn',
'name': 'gA',
'f_unique_weighted': 0.2,
'f_unique_to_query': 0.1,
'query_bp':100,
'unique_intersect_bp': 20,
'remaining_bp': 1,
'ksize': 31,
'scaled': 1}
if gather_dict is not None:
gatherD.update(gather_dict)
for col in exclude_cols:
gatherD.pop(col)
gatherRaw = GatherRow(**gatherD)
return gatherRaw
def make_TaxResult(gather_dict=None, taxD=None, keep_full_ident=False, keep_ident_version=False, skip_idents=None):
"""Make TaxResult from artificial gather row (dict)"""
gRow = make_GatherRow(gather_dict)
taxres = TaxResult(raw=gRow, keep_full_identifiers=keep_full_ident, keep_identifier_versions=keep_ident_version)
if taxD is not None:
taxres.get_match_lineage(tax_assignments=taxD, skip_idents=skip_idents)
return taxres
def make_QueryTaxResults(gather_info, taxD=None, single_query=False, keep_full_ident=False, keep_ident_version=False,
skip_idents=None, summarize=False, classify=False, classify_rank=None, c_thresh=0.1, ani_thresh=None):
"""Make QueryTaxResult(s) from artificial gather information, formatted as list of gather rows (dicts)"""
gather_results = {}
this_querytaxres = None
for gather_infoD in gather_info:
taxres = make_TaxResult(gather_infoD, taxD=taxD, keep_full_ident=keep_full_ident,
keep_ident_version=keep_ident_version, skip_idents=skip_idents)
query_name = taxres.query_name
# add to matching QueryTaxResult or create new one
if not this_querytaxres or not this_querytaxres.is_compatible(taxres):
# get existing or initialize new
this_querytaxres = gather_results.get(query_name, QueryTaxResult(taxres.query_info))
this_querytaxres.add_taxresult(taxres)
# print('missed_ident?', taxres.missed_ident)
gather_results[query_name] = this_querytaxres
if summarize:
for query_name, qres in gather_results.items():
qres.build_summarized_result()
if classify:
for query_name, qres in gather_results.items():
qres.build_classification_result(rank=classify_rank, containment_threshold=c_thresh, ani_threshold=ani_thresh)
# for convenience: If working with single query, just return that QueryTaxResult.
if single_query:
if len(gather_results.keys()) > 1:
raise ValueError("You passed in results for more than one query")
else:
return next(iter(gather_results.values()))
return gather_results
## tests
def test_ascending_taxlist_1():
assert list(ascending_taxlist()) == ['strain', 'species', 'genus', 'family', 'order', 'class', 'phylum', 'superkingdom']
def test_ascending_taxlist_2():
assert list(ascending_taxlist(include_strain=False)) == ['species', 'genus', 'family', 'order', 'class', 'phylum', 'superkingdom']
def test_QueryInfo_basic():
"basic functionality of QueryInfo dataclass"
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',query_n_hashes='10',ksize='31',scaled='10', total_weighted_hashes='200')
assert qInf.query_name == 'q1'
assert isinstance(qInf.query_n_hashes, int)
assert isinstance(qInf.ksize, int)
assert isinstance(qInf.scaled, int)
assert qInf.total_weighted_hashes == 200
assert qInf.total_weighted_bp == 2000
def test_QueryInfo_no_hash_info():
"QueryInfo dataclass for older gather results without query_n_hashes or total_weighted_hashes"
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',ksize=31,scaled=10)
assert qInf.query_name == 'q1'
assert qInf.query_n_hashes == 0
assert qInf.total_weighted_hashes == 0
assert qInf.total_weighted_bp == 0
def test_QueryInfo_missing():
"check that required args"
with pytest.raises(TypeError) as exc:
QueryInfo(query_name='q1', query_filename='f1',query_bp='100',query_n_hashes='10',ksize=31,scaled=10, total_weighted_hashes=200)
print(str(exc))
assert "missing 1 required positional argument: 'query_md5'" in str(exc)
def test_SummarizedGatherResult():
"basic functionality of SummarizedGatherResult dataclass"
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',
query_n_hashes='10',ksize='31',scaled='10', total_weighted_hashes='200')
sgr = SummarizedGatherResult(rank="phylum", fraction=0.2, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30)
print(sgr)
assert sgr.rank=='phylum'
sumD = sgr.as_summary_dict(query_info=qInf)
print(sumD)
assert sumD == {'rank': 'phylum', 'fraction': "0.2", 'lineage': 'a;b', 'f_weighted_at_rank': "0.3",
'bp_match_at_rank': "30", 'query_ani_at_rank': None, 'query_name': 'q1',
'query_md5': 'md5', 'query_filename': 'f1', 'total_weighted_hashes': "200"}
hD = sgr.as_human_friendly_dict(query_info=qInf)
print(hD)
assert hD == {'rank': 'phylum', 'fraction': '0.200', 'lineage': 'a;b', 'f_weighted_at_rank': '30.0%',
'bp_match_at_rank': "30", 'query_ani_at_rank': '- ', 'query_name': 'q1',
'query_md5': 'md5', 'query_filename': 'f1', 'total_weighted_hashes': "200"}
krD = sgr.as_kreport_dict(query_info=qInf)
print(krD)
assert krD == {'ncbi_taxid': None, 'sci_name': 'b', 'rank_code': 'P', 'num_bp_assigned': "0",
'percent_containment': '30.00', 'num_bp_contained': "600"}
lD = sgr.as_lineage_dict(ranks = RankLineageInfo().ranks, query_info=qInf)
print(lD)
assert lD == {'ident': 'q1', 'superkingdom': 'a', 'phylum': 'b', 'class': '', 'order': '',
'family': '', 'genus': '', 'species': '', 'strain': ''}
def test_SummarizedGatherResult_set_query_ani():
"Check ANI estimation within SummarizedGatherResult dataclass"
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',
query_n_hashes='10',ksize='31',scaled='10', total_weighted_hashes='200')
sgr = SummarizedGatherResult(rank="phylum", fraction=0.2, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30)
sgr.set_query_ani(query_info=qInf)
print(sgr.query_ani_at_rank)
assert sgr.query_ani_at_rank == approx(0.949, rel=1e-3)
# ANI can be calculated with query_bp OR query_n_hashes. Remove each and check the results are identical
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',
query_n_hashes=0,ksize='31',scaled='10', total_weighted_hashes='200')
sgr = SummarizedGatherResult(rank="phylum", fraction=0.2, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30)
sgr.set_query_ani(query_info=qInf)
print(sgr.query_ani_at_rank)
assert sgr.query_ani_at_rank == approx(0.949, rel=1e-3)
# try without query_bp
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp=0,
query_n_hashes='10',ksize='31',scaled='10', total_weighted_hashes='200')
sgr = SummarizedGatherResult(rank="phylum", fraction=0.2, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30)
sgr.set_query_ani(query_info=qInf)
print(sgr.query_ani_at_rank)
assert sgr.query_ani_at_rank == approx(0.949, rel=1e-3)
def test_SummarizedGatherResult_greater_than_1():
"basic functionality of SummarizedGatherResult dataclass"
# fraction > 1
with pytest.raises(ValueError) as exc:
SummarizedGatherResult(rank="phylum", fraction=0.3, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=1.2, bp_match_at_rank=30)
print(str(exc))
assert "> 100% of the query!" in str(exc)
# f_weighted > 1
with pytest.raises(ValueError) as exc:
SummarizedGatherResult(rank="phylum", fraction=1.2, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30)
print(str(exc))
assert "> 100% of the query!" in str(exc)
def test_SummarizedGatherResult_0_fraction():
with pytest.raises(ValueError) as exc:
SummarizedGatherResult(rank="phylum", fraction=-.1, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30)
err_msg = "Summarized fraction is <=0% of the query! This should not occur."
assert err_msg in str(exc)
#assert cr.status == 'nomatch'
with pytest.raises(ValueError) as exc:
SummarizedGatherResult(rank="phylum", fraction=.1, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0, bp_match_at_rank=30)
print(str(exc))
assert err_msg in str(exc)
def test_SummarizedGatherResult_species_kreport():
"basic functionality of SummarizedGatherResult dataclass"
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',
query_n_hashes='10',ksize='31',scaled='10', total_weighted_hashes='200')
sgr = SummarizedGatherResult(rank="species", fraction=0.2, lineage=RankLineageInfo(lineage_str="a;b;c;d;e;f;g"),
f_weighted_at_rank=0.3, bp_match_at_rank=30)
print(sgr)
assert sgr.rank=='species'
krD = sgr.as_kreport_dict(query_info=qInf)
print(krD)
assert krD == {'ncbi_taxid': None, 'sci_name': 'g', 'rank_code': 'S', 'num_bp_assigned': "600",
'percent_containment': '30.00', 'num_bp_contained': "600"}
def test_SummarizedGatherResult_summary_dict_limit_float():
"basic functionality of SummarizedGatherResult dataclass"
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',
query_n_hashes='10',ksize='31',scaled='10', total_weighted_hashes='200')
sgr = SummarizedGatherResult(rank="phylum", fraction=0.123456, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.345678, bp_match_at_rank=30)
print(sgr)
assert sgr.rank=='phylum'
sumD = sgr.as_summary_dict(query_info=qInf)
print(sumD)
assert sumD == {'rank': 'phylum', 'fraction': "0.123456", 'lineage': 'a;b', 'f_weighted_at_rank': "0.345678",
'bp_match_at_rank': "30", 'query_ani_at_rank': None, 'query_name': 'q1',
'query_md5': 'md5', 'query_filename': 'f1', 'total_weighted_hashes': "200"}
sumD = sgr.as_summary_dict(query_info=qInf, limit_float=True)
print(sumD)
assert sumD == {'rank': 'phylum', 'fraction': "0.123", 'lineage': 'a;b', 'f_weighted_at_rank': "0.346",
'bp_match_at_rank': "30", 'query_ani_at_rank': None, 'query_name': 'q1',
'query_md5': 'md5', 'query_filename': 'f1', 'total_weighted_hashes': "200"}
def test_ClassificationResult():
"basic functionality of ClassificationResult dataclass"
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',
query_n_hashes='10',ksize='31',scaled='10', total_weighted_hashes='200')
cr = ClassificationResult(rank="phylum", fraction=0.2, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30, query_ani_at_rank=0.97)
cr.set_status(query_info=qInf, containment_threshold=0.1)
assert cr.status == 'match'
print(cr.query_ani_at_rank)
assert cr.query_ani_at_rank == approx(0.949, rel=1e-3)
cr.set_status(query_info=qInf, containment_threshold=0.35)
assert cr.status == 'below_threshold'
lD = cr.as_lineage_dict(ranks = RankLineageInfo().ranks, query_info=qInf)
print(lD)
assert lD == {'ident': 'q1', 'superkingdom': 'a', 'phylum': 'b', 'class': '', 'order': '',
'family': '', 'genus': '', 'species': '', 'strain': ''}
def test_ClassificationResult_greater_than_1():
"basic functionality of SummarizedGatherResult dataclass"
# fraction > 1
with pytest.raises(ValueError) as exc:
ClassificationResult(rank="phylum", fraction=0.3, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=1.2, bp_match_at_rank=30)
print(str(exc))
assert "> 100% of the query!" in str(exc)
# f_weighted > 1
with pytest.raises(ValueError) as exc:
ClassificationResult(rank="phylum", fraction=1.2, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30)
print(str(exc))
assert "> 100% of the query!" in str(exc)
def test_ClassificationResult_0_fraction():
with pytest.raises(ValueError) as exc:
ClassificationResult(rank="phylum", fraction=-.1, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30)
err_msg = "Summarized fraction is <=0% of the query! This should not occur."
assert err_msg in str(exc)
#assert cr.status == 'nomatch'
with pytest.raises(ValueError) as exc:
ClassificationResult(rank="phylum", fraction=.1, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0, bp_match_at_rank=30)
print(str(exc))
assert err_msg in str(exc)
def test_ClassificationResult_build_krona_result():
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',
query_n_hashes='10',ksize='31',scaled='10', total_weighted_hashes='200')
cr = ClassificationResult(rank="phylum", fraction=0.2, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30, query_ani_at_rank=0.97)
#cr.set_status(query_info=qInf, rank='phylum')
kr, ukr = cr.build_krona_result(rank='phylum')
print(kr)
assert kr == (0.2, 'a', 'b')
print(ukr)
assert ukr == (0.8, 'unclassified', 'unclassified')
def test_ClassificationResult_build_krona_result_no_rank():
qInf = QueryInfo(query_name='q1', query_md5='md5', query_filename='f1',query_bp='100',
query_n_hashes='10',ksize='31',scaled='10', total_weighted_hashes='200')
cr = ClassificationResult(rank="phylum", fraction=0.2, lineage=RankLineageInfo(lineage_str="a;b"),
f_weighted_at_rank=0.3, bp_match_at_rank=30, query_ani_at_rank=0.97)
cr.set_status(query_info=qInf, containment_threshold=0.1)
def test_GatherRow_old_gather():
# gather does not contain query_name column
gA = {"name": "gA.1 name"}
with pytest.raises(TypeError) as exc:
make_GatherRow(gA, exclude_cols=['query_bp'])
print(str(exc))
assert "__init__() missing 1 required positional argument: 'query_bp'" in str(exc)
def test_get_ident_default():
ident = "GCF_001881345.1"
n_id = get_ident(ident)
assert n_id == "GCF_001881345"
def test_TaxResult_get_ident_default():
gA = {"name": "GCF_001881345.1"} # gather result with match name as GCF_001881345.1
taxres = make_TaxResult(gA)
print(taxres.match_ident)
assert taxres.match_ident == "GCF_001881345"
def test_get_ident_split_but_keep_version():
ident = "GCF_001881345.1 secondname"
n_id = get_ident(ident, keep_identifier_versions=True)
assert n_id == "GCF_001881345.1"
def test_TaxResult_get_ident_split_but_keep_version():
gA = {"name": "GCF_001881345.1 secondname"}
taxres = make_TaxResult(gA, keep_ident_version=True)
print("raw ident: ", taxres.raw.name)
print("keep_full?: ", taxres.keep_full_identifiers)
print("keep_version?: ",taxres.keep_identifier_versions)
print("final ident: ", taxres.match_ident)
assert taxres.match_ident == "GCF_001881345.1"
def test_get_ident_no_split():
ident = "GCF_001881345.1 secondname"
n_id = get_ident(ident, keep_full_identifiers=True)
assert n_id == "GCF_001881345.1 secondname"
def test_TaxResult_get_ident_keep_full():
gA = {"name": "GCF_001881345.1 secondname"}
taxres = make_TaxResult(gA, keep_full_ident=True)
print("raw ident: ", taxres.raw.name)
print("keep_full?: ", taxres.keep_full_identifiers)
print("keep_version?: ",taxres.keep_identifier_versions)
print("final ident: ", taxres.match_ident)
assert taxres.match_ident == "GCF_001881345.1 secondname"
def test_collect_gather_csvs(runtmp):
g_csv = utils.get_test_data('tax/test1.gather.csv')
from_file = runtmp.output("tmp-from-file.txt")
with open(from_file, 'w') as fp:
fp.write(f"{g_csv}\n")
gather_files = collect_gather_csvs([g_csv], from_file=from_file)
print("gather_files: ", gather_files)
assert len(gather_files) == 1
assert basename(gather_files[0]) == 'test1.gather.csv'
def test_check_and_load_gather_csvs_empty(runtmp):
g_res = runtmp.output('empty.gather.csv')
with open(g_res, 'w') as fp:
fp.write("")
csvs = [g_res]
# load taxonomy csv
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_assign = MultiLineageDB.load([taxonomy_csv], keep_full_identifiers=1)
print(tax_assign)
# check gather results and missing ids
with pytest.raises(Exception) as exc:
check_and_load_gather_csvs(csvs, tax_assign)
assert "Cannot read gather results from" in str(exc.value)
def test_check_and_load_gather_csvs_with_empty_force(runtmp):
g_csv = utils.get_test_data('tax/test1.gather.csv')
# make gather results with taxonomy name not in tax_assign
g_res2 = runtmp.output('gA.gather.csv')
g_results = [x.replace("GCF_001881345.1", "gA") for x in open(g_csv, 'r')]
with open(g_res2, 'w') as fp:
for line in g_results:
fp.write(line)
# make empty gather results
g_res3 = runtmp.output('empty.gather.csv')
with open(g_res3, 'w') as fp:
fp.write("")
csvs = [g_res2, g_res3]
# load taxonomy csv
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_assign = MultiLineageDB.load([taxonomy_csv],
keep_full_identifiers=False,
keep_identifier_versions=False)
print(tax_assign)
# check gather results and missing ids
gather_results = check_and_load_gather_csvs(csvs, tax_assign, force=True)
assert len(gather_results) == 1
q_res = gather_results[0]
assert len(q_res.raw_taxresults) == 4
assert q_res.n_missed == 1
assert 'gA' in q_res.missed_idents
assert q_res.n_skipped == 0
def test_check_and_load_gather_lineage_csvs_empty(runtmp):
# try loading an empty annotated gather file
g_res = runtmp.output('empty.gather-tax.csv')
with open(g_res, 'w') as fp:
fp.write("")
with pytest.raises(ValueError) as exc:
tax_assign = LineageDB.load_from_gather_with_lineages(g_res)
assert "cannot read taxonomy assignments" in str(exc.value)
def test_check_and_load_gather_lineage_csvs_bad_header(runtmp):
# test on file with wrong headers
g_res = runtmp.output('empty.gather-tax.csv')
with open(g_res, 'w', newline="") as fp:
fp.write("x,y,z")
with pytest.raises(ValueError) as exc:
tax_assign = LineageDB.load_from_gather_with_lineages(g_res)
assert "Expected headers 'name' and 'lineage' not found. Is this a with-lineages file?" in str(exc.value)
def test_check_and_load_gather_lineage_csvs_dne(runtmp):
# test loading with-lineage file that does not exist
g_res = runtmp.output('empty.gather-tax.csv')
with pytest.raises(ValueError) as exc:
tax_assign = LineageDB.load_from_gather_with_lineages(g_res)
assert "does not exist" in str(exc.value)
def test_check_and_load_gather_lineage_csvs_isdir(runtmp):
# test loading a with-lineage file that is actually a directory
g_res = runtmp.output('empty.gather-tax.csv')
os.mkdir(g_res)
with pytest.raises(ValueError) as exc:
tax_assign = LineageDB.load_from_gather_with_lineages(g_res)
assert "is a directory" in str(exc.value)
def test_check_and_load_gather_csvs_fail_on_missing(runtmp):
g_csv = utils.get_test_data('tax/test1.gather.csv')
# make gather results with taxonomy name not in tax_assign
g_res2 = runtmp.output('gA.gather.csv')
g_results = [x.replace("GCF_001881345.1", "gA") for x in open(g_csv, 'r')]
with open(g_res2, 'w') as fp:
for line in g_results:
fp.write(line)
csvs = [g_res2]
# load taxonomy csv
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_assign = MultiLineageDB.load([taxonomy_csv], keep_full_identifiers=1)
print(tax_assign)
# check gather results and missing ids
with pytest.raises(ValueError) as exc:
check_and_load_gather_csvs(csvs, tax_assign, fail_on_missing_taxonomy=True, force=True)
assert "Failing, as requested via --fail-on-missing-taxonomy" in str(exc)
def test_load_gather_results():
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_assign = MultiLineageDB.load([taxonomy_csv],
keep_full_identifiers=False,
keep_identifier_versions=False)
gather_csv = utils.get_test_data('tax/test1.gather.csv')
gather_results, header = load_gather_results(gather_csv, tax_assignments=tax_assign)
assert len(gather_results) == 1
for query_name, res in gather_results.items():
assert query_name == 'test1'
assert len(res.raw_taxresults) == 4
def test_load_gather_results_gzipped(runtmp):
gather_csv = utils.get_test_data('tax/test1.gather.csv')
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_assign = MultiLineageDB.load([taxonomy_csv],
keep_full_identifiers=False,
keep_identifier_versions=False)
gather_csv = utils.get_test_data('tax/test1.gather.csv')
# rewrite gather_csv as gzipped csv
gz_gather = runtmp.output('g.csv.gz')
with open(gather_csv, 'rb') as f_in, gzip.open(gz_gather, 'wb') as f_out:
f_out.writelines(f_in)
#gather_results, header, seen_queries = load_gather_results(gz_gather)
gather_results, header = load_gather_results(gz_gather, tax_assignments=tax_assign)
assert len(gather_results) == 1
for query_name, res in gather_results.items():
assert query_name == 'test1'
assert len(res.raw_taxresults) == 4
def test_load_gather_results_bad_header(runtmp):
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_assign = MultiLineageDB.load([taxonomy_csv],
keep_full_identifiers=False,
keep_identifier_versions=False)
g_csv = utils.get_test_data('tax/test1.gather.csv')
bad_g_csv = runtmp.output('g.csv')
#creates bad gather result
bad_g = [x.replace("f_unique_to_query", "nope") for x in open(g_csv, 'r')]
with open(bad_g_csv, 'w') as fp:
for line in bad_g:
fp.write(line)
print("bad_gather_results: \n", bad_g)
with pytest.raises(ValueError) as exc:
gather_results, header = load_gather_results(bad_g_csv, tax_assignments=tax_assign)
assert f"'{bad_g_csv}' is missing columns needed for taxonomic summarization" in str(exc.value)
def test_load_gather_results_empty(runtmp):
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_assign = MultiLineageDB.load([taxonomy_csv],
keep_full_identifiers=False,
keep_identifier_versions=False)
empty_csv = runtmp.output('g.csv')
#creates empty gather result
with open(empty_csv, 'w') as fp:
fp.write('')
with pytest.raises(ValueError) as exc:
gather_results, header = load_gather_results(empty_csv, tax_assignments=tax_assign)
assert f"Cannot read gather results from '{empty_csv}'. Is file empty?" in str(exc.value)
def test_load_taxonomy_csv():
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_assign = MultiLineageDB.load([taxonomy_csv])
print("taxonomy assignments: \n", tax_assign)
assert list(tax_assign.keys()) == ['GCF_001881345.1', 'GCF_009494285.1', 'GCF_013368705.1', 'GCF_003471795.1', 'GCF_000017325.1', 'GCF_000021665.1']
assert len(tax_assign) == 6 # should have read 6 rows
def test_load_taxonomy_csv_gzip(runtmp):
# test loading a gzipped taxonomy csv file
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_gz = runtmp.output('tax.csv.gz')
with gzip.open(tax_gz, 'wt') as outfp:
with open(taxonomy_csv, 'rt') as infp:
data = infp.read()
outfp.write(data)
tax_assign = MultiLineageDB.load([tax_gz])
print("taxonomy assignments: \n", tax_assign)
assert list(tax_assign.keys()) == ['GCF_001881345.1', 'GCF_009494285.1', 'GCF_013368705.1', 'GCF_003471795.1', 'GCF_000017325.1', 'GCF_000021665.1']
assert len(tax_assign) == 6 # should have read 6 rows
def test_load_taxonomy_csv_split_id():
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
tax_assign = MultiLineageDB.load([taxonomy_csv], keep_full_identifiers=0,
keep_identifier_versions=False)
print("taxonomy assignments: \n", tax_assign)
assert list(tax_assign.keys()) == ['GCF_001881345', 'GCF_009494285', 'GCF_013368705', 'GCF_003471795', 'GCF_000017325', 'GCF_000021665']
assert len(tax_assign) == 6 # should have read 6 rows
def test_load_taxonomy_csv_with_ncbi_id(runtmp):
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
upd_csv = runtmp.output("updated_taxonomy.csv")
with open(upd_csv, 'w') as new_tax:
tax = [x.rstrip() for x in open(taxonomy_csv, 'r')]
ncbi_id = "ncbi_id after_space"
fake_lin = [ncbi_id] + ["sk", "phy", "cls", "ord", "fam", "gen", "sp"]
ncbi_tax = ",".join(fake_lin)
tax.append(ncbi_tax)
new_tax.write("\n".join(tax))
tax_assign = MultiLineageDB.load([upd_csv], keep_full_identifiers=True)
print("taxonomy assignments: \n", tax_assign)
assert list(tax_assign.keys()) == ['GCF_001881345.1', 'GCF_009494285.1', 'GCF_013368705.1', 'GCF_003471795.1', 'GCF_000017325.1', 'GCF_000021665.1', "ncbi_id after_space"]
assert len(tax_assign) == 7 # should have read 7 rows
def test_load_taxonomy_csv_split_id_ncbi(runtmp):
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
upd_csv = runtmp.output("updated_taxonomy.csv")
with open(upd_csv, 'w') as new_tax:
tax = [x.rstrip() for x in open(taxonomy_csv, 'r')]
ncbi_id = "ncbi_id after_space"
fake_lin = [ncbi_id] + ["sk", "phy", "cls", "ord", "fam", "gen", "sp"]
ncbi_tax = ",".join(fake_lin)
tax.append(ncbi_tax)
new_tax.write("\n".join(tax))
tax_assign = MultiLineageDB.load([upd_csv], keep_full_identifiers=False,
keep_identifier_versions=False)
print("taxonomy assignments: \n", tax_assign)
assert list(tax_assign.keys()) == ['GCF_001881345', 'GCF_009494285', 'GCF_013368705', 'GCF_003471795', 'GCF_000017325', 'GCF_000021665', "ncbi_id"]
assert len(tax_assign) == 7 # should have read 7 rows
# check for non-sensical args.
with pytest.raises(ValueError):
tax_assign = MultiLineageDB.load([upd_csv], keep_full_identifiers=1,
keep_identifier_versions=False)
def test_load_taxonomy_csv_duplicate(runtmp):
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
duplicated_csv = runtmp.output("duplicated_taxonomy.csv")
with open(duplicated_csv, 'w') as dup:
tax = [x.rstrip() for x in open(taxonomy_csv, 'r')]
tax.append(tax[1] + 'FOO') # add first tax_assign again
print(tax[-1])
dup.write("\n".join(tax))
with pytest.raises(Exception) as exc:
MultiLineageDB.load([duplicated_csv])
assert "cannot read taxonomy assignments" in str(exc.value)
assert "multiple lineages for identifier GCF_001881345.1" in str(exc.value)
def test_load_taxonomy_csv_duplicate_force(runtmp):
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
duplicated_csv = runtmp.output("duplicated_taxonomy.csv")
with open(duplicated_csv, 'w') as dup:
tax = [x.rstrip() for x in open(taxonomy_csv, 'r')]
tax.append(tax[1]) # add first tax_assign again
dup.write("\n".join(tax))
# now force
tax_assign = MultiLineageDB.load([duplicated_csv], force=True)
print("taxonomy assignments: \n", tax_assign)
assert list(tax_assign.keys()) == ['GCF_001881345.1', 'GCF_009494285.1', 'GCF_013368705.1', 'GCF_003471795.1', 'GCF_000017325.1', 'GCF_000021665.1']
def test_format_for_krona_summarization():
"""test format for krona"""
# make gather results
# make mini taxonomy
gA_tax = ("gA", "a;b")
gB_tax = ("gB", "a;c")
taxD = make_mini_taxonomy([gA_tax,gB_tax])
gather_results = [{'query_name': 'queryA', 'name': 'gA', 'f_unique_weighted': 0.2,'f_unique_to_query': 0.2,'unique_intersect_bp': 50},
{'query_name': 'queryA', "name": 'gB', 'f_unique_weighted': 0.3,'f_unique_to_query': 0.3,'unique_intersect_bp': 30}]
q_res = make_QueryTaxResults(gather_info=gather_results, taxD=taxD, summarize=True, single_query=True)
kres, header = format_for_krona([q_res], 'superkingdom')
assert header == ['fraction', 'superkingdom']
print("krona_res: ", kres)
assert kres == [(0.5, 'a'), (0.5, 'unclassified')]
kres, header = format_for_krona([q_res], 'phylum')
assert header == ['fraction', 'superkingdom', 'phylum']
assert kres == [(0.3, 'a', 'c'), (0.2, 'a', 'b'), (0.5, 'unclassified', 'unclassified')]
def test_format_for_krona_classification():
"""test format for krona"""
# make gather results
# make mini taxonomy
gA_tax = ("gA", "a;b")
gB_tax = ("gB", "a;c")
taxD = make_mini_taxonomy([gA_tax,gB_tax])
gather_results = [{'query_name': 'queryA', 'name': 'gA', 'f_unique_weighted': 0.2,'f_unique_to_query': 0.2,'unique_intersect_bp': 50},
{'query_name': 'queryA', "name": 'gB', 'f_unique_weighted': 0.3,'f_unique_to_query': 0.3,'unique_intersect_bp': 30}]
q_res = make_QueryTaxResults(gather_info=gather_results, taxD=taxD, classify=True, single_query=True)
kres, header = format_for_krona([q_res], 'superkingdom', classification=True)
assert header == ['fraction', 'superkingdom']
print("krona_res: ", kres)
assert kres == [(0.5, 'a')]#, (0.5, 'unclassified')]
kres, header = format_for_krona([q_res], 'phylum', classification=True)
assert header == ['fraction', 'superkingdom', 'phylum']
assert kres == [(0.3, 'a', 'c')]#, (0.7, 'unclassified', 'unclassified')]
def test_format_for_krona_improper_rank():
"""test format for krona"""
# make gather results
# make mini taxonomy
gA_tax = ("gA", "a;b")
gB_tax = ("gB", "a;c")
taxD = make_mini_taxonomy([gA_tax,gB_tax])
gather_results = [{'query_name': 'queryA', 'name': 'gA', 'f_unique_weighted': 0.2,'f_unique_to_query': 0.2,'unique_intersect_bp': 50},
{'query_name': 'queryA', "name": 'gB', 'f_unique_weighted': 0.3,'f_unique_to_query': 0.3,'unique_intersect_bp': 30}]
q_res = make_QueryTaxResults(gather_info=gather_results, taxD=taxD, summarize=True, single_query=True)
with pytest.raises(ValueError) as exc:
format_for_krona([q_res], 'NotARank')
print(str(exc))
assert "Rank 'NotARank' not present in summarized ranks." in str(exc)
def test_format_for_krona_summarization_two_queries():
"""test format for krona with multiple queries (normalize by n_queries)"""
# make gather results
# make mini taxonomy
gA_tax = ("gA", "a;b")
gB_tax = ("gB", "a;c")
taxD = make_mini_taxonomy([gA_tax,gB_tax])
gather_results = [{'query_name': 'queryA', 'name': 'gA', 'f_unique_weighted': 0.2,'f_unique_to_query': 0.2,'unique_intersect_bp': 50},
{'query_name': 'queryA', "name": 'gB', 'f_unique_weighted': 0.3,'f_unique_to_query': 0.3,'unique_intersect_bp': 30},
{'query_name': 'queryB', "name": 'gB', 'f_unique_weighted': 0.5,'f_unique_to_query': 0.5,'unique_intersect_bp': 50}]
gres = make_QueryTaxResults(gather_info=gather_results, taxD=taxD, summarize=True)
kres, header = format_for_krona(list(gres.values()), 'superkingdom')
assert header == ['fraction', 'superkingdom']
print("krona_res: ", kres)
assert kres == [(0.5, 'a'), (0.5, 'unclassified')]
kres, header = format_for_krona(list(gres.values()), 'phylum')
assert header == ['fraction', 'superkingdom', 'phylum']
assert kres == [(0.4, 'a', 'c'), (0.1, 'a', 'b'), (0.5, 'unclassified', 'unclassified')]
def test_write_krona(runtmp):
"""test two matches, equal f_unique_to_query"""
krona_results = [(0.5, 'a', 'b', 'c'), (0.5, 'a', 'b', 'd')]
header = ['fraction', 'superkingdom', 'phylum', 'class']
outk= runtmp.output("outkrona.tsv")
with open(outk, 'w') as out_fp:
write_krona(header, krona_results, out_fp)
kr = [x.strip().split('\t') for x in open(outk, 'r')]
print("krona_results_from_file: \n", kr)
assert kr[0] == ["fraction", "superkingdom", "phylum", "class"]
assert kr[1] == ["0.5", "a", "b", "c"]
assert kr[2] == ["0.5", "a", "b", "d"]
def test_write_lineage_sample_frac(runtmp):
outfrac = runtmp.output('outfrac.csv')
sample_names = ['sample1', 'sample2']
sk_linD = {'a': {'sample1': '0.500' ,'sample2': '0.700'}}
with open(outfrac, 'w') as out_fp:
write_lineage_sample_frac(sample_names, sk_linD, out_fp)
frac_lines = [x.strip().split('\t') for x in open(outfrac, 'r')]
print("csv_lines: ", frac_lines)
assert frac_lines == [['lineage', 'sample1', 'sample2'], ['a', '0.500', '0.700']]
phy_linD = {'a;b': {'sample1': '0.500'}, 'a;c': {'sample2': '0.700'}}
with open(outfrac, 'w') as out_fp:
write_lineage_sample_frac(sample_names, phy_linD, out_fp)
frac_lines = [x.strip().split('\t') for x in open(outfrac, 'r')]
print("csv_lines: ", frac_lines)
assert frac_lines == [['lineage', 'sample1', 'sample2'], ['a;b', '0.500', '0'], ['a;c', '0', '0.700']]
def test_write_lineage_sample_frac_format_lineage(runtmp):
outfrac = runtmp.output('outfrac.csv')
sample_names = ['sample1', 'sample2']
sk_lineage='a'
print(sk_lineage)
sk_linD = {sk_lineage: {'sample1': '0.500' ,'sample2': '0.700'}}
with open(outfrac, 'w') as out_fp:
write_lineage_sample_frac(sample_names, sk_linD, out_fp)
frac_lines = [x.strip().split('\t') for x in open(outfrac, 'r')]
print("csv_lines: ", frac_lines)
assert frac_lines == [['lineage', 'sample1', 'sample2'], ['a', '0.500', '0.700']]
phy_lineage='a;b'
print(phy_lineage)
phy2_lineage = 'a;c'
print(phy2_lineage)
phy_linD = {phy_lineage: {'sample1': '0.500'}, phy2_lineage: {'sample2': '0.700'}}
with open(outfrac, 'w') as out_fp:
write_lineage_sample_frac(sample_names, phy_linD, out_fp)
frac_lines = [x.strip().split('\t') for x in open(outfrac, 'r')]
print("csv_lines: ", frac_lines)
assert frac_lines == [['lineage', 'sample1', 'sample2'], ['a;b', '0.500', '0'], ['a;c', '0', '0.700']]
def test_tax_multi_load_files(runtmp):
# test loading various good and bad files
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
taxonomy_csv2 = utils.get_test_data('tax/test-strain.taxonomy.csv')
badcsv = utils.get_test_data('tax/47+63_x_gtdb-rs202.gather.csv')
db = MultiLineageDB.load([taxonomy_csv])
assert len(db) == 6
assert 'strain' not in db.available_ranks
db = MultiLineageDB.load([taxonomy_csv2])
assert len(db) == 6
assert 'strain' in db.available_ranks
assert db['GCF_001881345.1'][0].rank == 'superkingdom'
# load a string rather than a list
with pytest.raises(TypeError):
MultiLineageDB.load(badcsv)
# load a bad CSV
with pytest.raises(ValueError):
MultiLineageDB.load([badcsv])
# load a directory
with pytest.raises(ValueError):
MultiLineageDB.load([runtmp.output('')])
# file does not exist
with pytest.raises(ValueError):
MultiLineageDB.load([runtmp.output('no-such-file')])
def test_tax_sql_load_new_file(runtmp):
# test loading a newer-format sql file with sourmash_internals table
taxonomy_db = utils.get_test_data('sqlite/test.taxonomy.db')
db = MultiLineageDB.load([taxonomy_db])
print(list(db.keys()))
assert len(db) == 6
assert 'strain' not in db.available_ranks
assert db['GCF_001881345'][0].rank == 'superkingdom'
def test_tax_multi_load_files_shadowed(runtmp):
# test loading various good and bad files
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
taxonomy_csv2 = utils.get_test_data('tax/test-strain.taxonomy.csv')
taxonomy_db = utils.get_test_data('tax/test.taxonomy.db')
db = MultiLineageDB.load([taxonomy_csv, taxonomy_csv2, taxonomy_db],
keep_full_identifiers=False,
keep_identifier_versions=False)
assert len(db.shadowed_identifiers()) == 6
# we should have everything including strain
assert set(lca_utils.taxlist()) == set(db.available_ranks)
db = MultiLineageDB.load([taxonomy_csv, taxonomy_db],
keep_full_identifiers=False,
keep_identifier_versions=False)
assert len(db.shadowed_identifiers()) == 6
assert set(lca_utils.taxlist(include_strain=False)) == set(db.available_ranks)
def test_tax_multi_save_files(runtmp, keep_identifiers, keep_versions):
# test save
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
if keep_identifiers and not keep_versions:
with pytest.raises(ValueError):
db = MultiLineageDB.load([taxonomy_csv],
keep_full_identifiers=keep_identifiers,
keep_identifier_versions=keep_versions)
return
db = MultiLineageDB.load([taxonomy_csv],
keep_full_identifiers=keep_identifiers,
keep_identifier_versions=keep_versions)
out_db = runtmp.output('out.db')
out_csv = runtmp.output('out.csv')
out2_csv = runtmp.output('out2.csv')
# can't save to fp with sql
with open(out_csv, 'wt') as fp:
with pytest.raises(ValueError):
db.save(fp, 'sql')
# these should all work...
with open(out_csv, 'wt') as fp:
db.save(fp, 'csv')
db.save(out2_csv, 'csv')
db.save(out_db, 'sql')
# ...and be equal
db1 = db.load([out_db])
db2 = db.load([out_csv])
db3 = db.load([out2_csv])
def strip_strain(it):
for k, v in it:
if v[-1].rank == 'strain':
v = v[:-1]
yield k, v
import pprint
db_items = list(strip_strain(db.items()))
db1_items = list(strip_strain(db1.items()))
db2_items = list(strip_strain(db2.items()))
db3_items = list(strip_strain(db3.items()))
pprint.pprint(db_items)
print('XXX')
pprint.pprint(list(db1_items))
print('XXX')
pprint.pprint(list(db2_items))
assert set(db_items) == set(db1_items)
assert set(db_items) == set(db2_items)
assert set(db_items) == set(db3_items)
def test_lineage_db_csv_load(runtmp):
# test LineageDB.load
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
taxonomy_csv2 = utils.get_test_data('tax/test-strain.taxonomy.csv')
badcsv = utils.get_test_data('tax/47+63_x_gtdb-rs202.gather.csv')
badcsv2 = utils.get_test_data('tax/test-missing-ranks.taxonomy.csv')
db = LineageDB.load(taxonomy_csv)
assert len(db) == 6
assert 'strain' not in db.available_ranks
db = LineageDB.load(taxonomy_csv2)
assert len(db) == 6
assert 'strain' in db.available_ranks
# load the wrong kind of csv
with pytest.raises(ValueError):
LineageDB.load(badcsv)
# load a bad CSV
with pytest.raises(ValueError):
LineageDB.load(badcsv2)
# load a directory
with pytest.raises(ValueError):
LineageDB.load(runtmp.output(''))
# file does not exist
with pytest.raises(ValueError):
LineageDB.load(runtmp.output('no-such-file'))
# construct a CSV with bad headers
with open(runtmp.output('xxx.csv'), 'w', newline="") as fp:
fp.write('x,y,z\n')
with pytest.raises(ValueError):
LineageDB.load(runtmp.output('xxx.csv'))
def test_lineage_db_sql_load(runtmp):
# test LineageDB_sqlite.load
taxonomy_db = utils.get_test_data('tax/test.taxonomy.db')
taxonomy_csv = utils.get_test_data('tax/test.taxonomy.csv')
db = LineageDB_Sqlite.load(taxonomy_db)
assert bool(db)
assert len(db) == 6
db.available_ranks
assert 'strain' not in db.available_ranks
assert db['GCF_001881345'][0].rank == 'superkingdom'
with pytest.raises(KeyError):
db['foo']
# load any kind of CSV
with pytest.raises(ValueError):
LineageDB_Sqlite.load(taxonomy_csv)
# load a directory
with pytest.raises(ValueError):
LineageDB_Sqlite.load(runtmp.output(''))
# file does not exist
with pytest.raises(ValueError):
LineageDB_Sqlite.load(runtmp.output('no-such-file'))
def test_LineagePair():
lin = LineagePair(rank="rank1", name='name1')