No output from example API

Fixes #91
Robaina · Sep 9, 2023 · b32df7d · b32df7d
1 parent 016ffb6
commit b32df7d
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Showing 11 changed files with 5,114 additions and 17 deletions.
diff --git a/.gitignore b/.gitignore
@@ -23,4 +23,5 @@ wiki/*
 examples/data/*
 examples/example_cli/*
 examples/example_api/*
-pyopensci_reviews/*
+pyopensci_reviews/*
+test_issue_91/*
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "pynteny"
-version = "1.1.0"
+version = "1.1.2"
 description = "Synteny-aware hmm searches made easy in Python"
 license = "Apache-2.0"
 authors = ["Semidán Robaina Estévez <srobaina@ull.edu.es>"]
@@ -18,14 +18,10 @@ classifiers = [
     "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python :: 3",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "Natural Language :: English"
-]
-packages = [
-    { include = "pynteny", from = "src" },
-]
-include = [
-    "src/pynteny/config.json"
+    "Natural Language :: English",
 ]
+packages = [{ include = "pynteny", from = "src" }]
+include = ["src/pynteny/config.json"]
 [tool.poetry.dependencies]
 python = "^3.8"
 [tool.poetry.scripts]

diff --git a/src/pynteny/filter.py b/src/pynteny/filter.py
@@ -191,7 +191,7 @@ def __init__(
             )
         )
         self._n_hmm_groups = len(self._parsed_structure["hmm_groups"])
-        self._n_hmms = len(self._hmms)  # len(self._hmm_order_dict)
+        self._n_hmms = len(self._hmm_order_dict)
         self._unordered = unordered
 
     def _in_hmm_group(self, query_hmm_group: str, hmm_group: str) -> bool:

diff --git a/tests/test_data/hmm_meta.tsv b/tests/test_data/hmm_meta.tsv
@@ -1,4 +1,8 @@
-#ncbi_accession	source_identifier	label	sequence_cutoff	domain_cutoff	hmm_length	family_type	for_structural_annotation	for_naming	for_AMRFinder	product_name	gene_symbol	ec_numbers	go_terms	pmids	taxonomic_range	taxonomic_range_name	taxonomic_rank_name	n_refseq_protein_hits	source	name_orig
-TIGR00170.1	TIGR00170	leuC	560.25	560.25	466	equivalog_domain	Y	Y	N	3-isopropylmalate dehydratase large subunit	leuC	4.2.1.33	GO:0003861,GO:0009098,GO:0009316		131567.0	cellular organisms	no rank	38458	JCVI	3-isopropylmalate dehydratase, large subunit
-TIGR00171.1	TIGR00171	leuD	116.25	116.25	188	equivalog_domain	Y	Y	N	3-isopropylmalate dehydratase small subunit	leuD	4.2.1.33	GO:0003861,GO:0009098,GO:0009316		131567.0	cellular organisms	no rank	33829	JCVI	3-isopropylmalate dehydratase, small subunit
-TIGR00973.1	TIGR00973	leuA	598.7	598.7	494	equivalog	Y	Y	N	2-isopropylmalate synthase	leuA	2.3.3.13	GO:0003852,GO:0009098		131567.0	cellular organisms	no rank	20500	JCVI	2-isopropylmalate synthase
+#ncbi_accession	label	product_name	gene_symbol	ec_numbers
+TIGR00171.1	leuD	3-isopropylmalate dehydratase small subunit	leuD	4.2.1.33
+TIGR02084.1	leuD	3-isopropylmalate dehydratase small subunit	leuD	4.2.1.33
+TIGR00170.1	leuC	3-isopropylmalate dehydratase large subunit	leuC	4.2.1.33
+TIGR02083.1	LEU2	3-isopropylmalate dehydratase large subunit	leuC	4.2.1.33
+TIGR00973.1	leuA_bact	2-isopropylmalate synthase	leuA	2.3.3.13
+NF002084.0	PRK00915.1-1	2-isopropylmalate synthase	leuA	2.3.3.13
+TIGR00970.1	leuA_yeast	2-isopropylmalate synthase	leuA	2.3.3.13
diff --git a/tests/test_data/hmms/NF002084.0.HMM b/tests/test_data/hmms/NF002084.0.HMM
diff --git a/tests/test_data/hmms/TIGR00970.1.HMM b/tests/test_data/hmms/TIGR00970.1.HMM
diff --git a/tests/test_data/hmms/TIGR02083.1.HMM b/tests/test_data/hmms/TIGR02083.1.HMM
diff --git a/tests/test_data/hmms/TIGR02084.1.HMM b/tests/test_data/hmms/TIGR02084.1.HMM
diff --git a/tests/test_hmm.py b/tests/test_hmm.py
@@ -32,7 +32,9 @@ def test_get_HMM_group_for_gene_symbol(self):
         pgap = PGAP(this_file_dir / "test_data/hmm_meta.tsv")
         hmm_group = pgap.get_HMM_group_for_gene_symbol("leuD")
         self.assertEqual(
-            hmm_group, "TIGR00171.1", "Failed to retrieve HMM group from gene symbol"
+            hmm_group,
+            "TIGR00171.1|TIGR02084.1",
+            "Failed to retrieve HMM group from gene symbol",
         )
 
     def test_get_meta_info_for_HMM(self):

diff --git a/tests/test_integration_search.py b/tests/test_integration_search.py
@@ -19,7 +19,7 @@ def test_search(self):
         with TemporaryDirectory() as tempdir:
             search = Search(
                 data=tests_dir / "test_data/MG1655.fasta",
-                synteny_struc="<TIGR00171.1 0 <TIGR00170.1 1 <TIGR00973.1",
+                synteny_struc="<(TIGR00171.1|TIGR02084.1) 0 <(TIGR00170.1|TIGR02083.1) 1 <(TIGR00973.1|NF002084.0|TIGR00970.1)",
                 hmm_dir=tests_dir / "test_data/hmms",
                 hmm_meta=None,
                 outdir=Path(tempdir),

diff --git a/tests/test_parser.py b/tests/test_parser.py
@@ -74,7 +74,7 @@ def test_parse_genes_in_synteny_structure(self):
         )
         self.assertEqual(
             parsed_struct,
-            "<TIGR00171.1 0 <TIGR00170.1 1 <TIGR00973.1",
+            "<(TIGR00171.1|TIGR02084.1) 0 <(TIGR00170.1|TIGR02083.1) 1 <(TIGR00973.1|NF002084.0|TIGR00970.1)",
             "Failed to parse gene symbols in synteny structure",
         )