RNApolis 0.3.5__tar.gz → 0.3.7__tar.gz

{RNApolis-0.3.5/src/RNApolis.egg-info → RNApolis-0.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.3.5
+Version: 0.3.7
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{RNApolis-0.3.5 → RNApolis-0.3.7}/setup.py

@@ -5,7 +5,7 @@ with open("README.md") as f:
 
 setup(
     name="RNApolis",
-    version="0.3.5",
+    version="0.3.7",
     packages=["rnapolis"],
     package_dir={"": "src"},
     author="Tomasz Zok",

{RNApolis-0.3.5 → RNApolis-0.3.7/src/RNApolis.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.3.5
+Version: 0.3.7
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{RNApolis-0.3.5 → RNApolis-0.3.7}/src/RNApolis.egg-info/SOURCES.txt

@@ -25,4 +25,5 @@ tests/test_common.py
 tests/test_metareader.py
 tests/test_parser.py
 tests/test_quadruplexes.py
+tests/test_rfam_folder.py
 tests/test_tertiary.py

{RNApolis-0.3.5 → RNApolis-0.3.7}/src/rnapolis/rfam_folder.py

@@ -137,7 +137,11 @@ def analyze_cmsearch(cmsearch: str, fasta: FASTA, count: int = 1):
         for i in range(len(structure)):
             if structure[i] != " ":
                 break
+
         j = structure.find(" CS")
+        while structure[j] == " ":
+            j -= 1
+        j += 1
 
         structure = structure[i:j]
         sequence = sequence[i:j].upper()
@@ -210,6 +214,15 @@ def analyze_cmsearch(cmsearch: str, fasta: FASTA, count: int = 1):
 
         assert len(sequence) == len(structure)
 
+        i = fasta.sequence.find(sequence)
+        structure = (
+            "." * i + structure + "." * (len(fasta.sequence) - len(sequence) - i)
+        )
+        sequence = fasta.sequence
+
+        assert len(sequence) == len(structure)
+        assert len(sequence) == len(fasta.sequence)
+
         structure = (
             structure.replace(":", ".")
             .replace("-", ".")

RNApolis-0.3.7/tests/test_rfam_folder.py

@@ -0,0 +1,21 @@
+import os
+
+import pytest
+
+from rnapolis.rfam_folder import generate_consensus_secondary_structure, parse_fasta
+
+IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true"
+
+
+@pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="Test doesn't work in Github Actions.")
+def test_GK000002():
+    fasta = parse_fasta("tests/GK000002.2-66269475-66272524.fa")
+    generate_consensus_secondary_structure(fasta[0], "RF02540", False)
+
+
+@pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="Test doesn't work in Github Actions.")
+def test_LJAJ01000009():
+    fasta = parse_fasta("tests/LJAJ01000009.1-42413-42384.fa")
+    result = generate_consensus_secondary_structure(fasta[0], "RF01315", False)
+    sequence = result[0].split("\n")[1]
+    assert len(sequence) == len(fasta[0].sequence)