86 wrong attribute type in msa (#87)

* API update * added type annotation for MSA * bump version * API update * removed api generation --------- Co-authored-by: sdRDM Bot <[email protected]>
PyEED · Jun 21, 2024 · 429557e · 429557e
1 parent 86069d9
commit 429557e
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Showing 18 changed files with 37 additions and 36 deletions.
diff --git a/.github/workflows/generate_api.yaml b/.github/workflows/generate_api.yaml
diff --git a/pyeed/align/msa.py b/pyeed/align/msa.py
@@ -1,17 +1,16 @@
-from typing import List
-
 from Bio.Align import MultipleSeqAlignment
 from pydantic import BaseModel, Field
 from rich.console import Console
 from rich.status import Status
 
 from pyeed.core.alignmentresult import AlignmentResult
+from pyeed.core.proteinrecord import ProteinRecord
 from pyeed.core.sequence import Sequence
 from pyeed.tools.clustalo import ClustalOmega
 
 
 class MSA(BaseModel):
-    sequences: List[Sequence] = Field(
+    sequences: list[Sequence | ProteinRecord] = Field(
         ...,
         description="List of sequences to be aligned.",
         min_length=2,
@@ -47,14 +46,25 @@ def _map_alignment(self, alignment: MultipleSeqAlignment) -> AlignmentResult:
         """
 
         result = AlignmentResult()
-        [result.add_to_sequences(id=seq.id, sequence=seq.sequence, sequence_id=seq.id) for seq in self.sequences]
-        [result.add_to_aligned_sequences(id=seq.id, sequence=str(seq.seq), sequence_id=seq.id) for seq in alignment]
+        [
+            result.add_to_sequences(
+                id=seq.id, sequence=seq.sequence, sequence_id=seq.id
+            )
+            for seq in self.sequences
+        ]
+        [
+            result.add_to_aligned_sequences(
+                id=seq.id, sequence=str(seq.seq), sequence_id=seq.id
+            )
+            for seq in alignment
+        ]
 
         return result
 
 
 if __name__ == "__main__":
     from pyeed.core.proteinrecord import ProteinRecord
+    from pyeed.core.sequence import Sequence
 
     protein1 = ProteinRecord(
         id="seq1",
@@ -68,7 +78,12 @@ def _map_alignment(self, alignment: MultipleSeqAlignment) -> AlignmentResult:
         id="seq3",
         sequence="MTHKILLLTLLFTLLFSSCYSRG",
     )
-    sequences = [protein1, protein2, protein3]
+    protein4 = Sequence(
+        id="seq4",
+        sequence="AAAAAAA",
+    )
+
+    sequences = [protein1, protein2, protein3, protein4]
 
     msa = MSA(sequences=sequences)
     alignment = msa.clustalo()

diff --git a/pyeed/core/abstractannotation.py b/pyeed/core/abstractannotation.py
@@ -49,7 +49,7 @@ class AbstractAnnotation(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/alignmentresult.py b/pyeed/core/alignmentresult.py
@@ -61,7 +61,7 @@ class AlignmentResult(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/blastdata.py b/pyeed/core/blastdata.py
@@ -90,7 +90,7 @@ class BlastData(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/clustalomegaresult.py b/pyeed/core/clustalomegaresult.py
@@ -32,7 +32,7 @@ class ClustalOmegaResult(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/dnarecord.py b/pyeed/core/dnarecord.py
@@ -32,7 +32,7 @@ class DNARecord(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/numberedsequence.py b/pyeed/core/numberedsequence.py
@@ -40,7 +40,7 @@ class NumberedSequence(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/organism.py b/pyeed/core/organism.py
@@ -108,7 +108,7 @@ class Organism(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/pairwisealignmentresult.py b/pyeed/core/pairwisealignmentresult.py
@@ -60,7 +60,7 @@ class PairwiseAlignmentResult(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/proteinrecord.py b/pyeed/core/proteinrecord.py
@@ -75,7 +75,7 @@ class ProteinRecord(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/region.py b/pyeed/core/region.py
@@ -43,7 +43,7 @@ class Region(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/regionset.py b/pyeed/core/regionset.py
@@ -35,7 +35,7 @@ class RegionSet(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _object_terms: Set[str] = PrivateAttr(

diff --git a/pyeed/core/sequence.py b/pyeed/core/sequence.py
@@ -38,7 +38,7 @@ class Sequence(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/sequencerecord.py b/pyeed/core/sequencerecord.py
@@ -103,7 +103,7 @@ class SequenceRecord(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/site.py b/pyeed/core/site.py
@@ -35,7 +35,7 @@ class Site(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyeed/core/standardnumbering.py b/pyeed/core/standardnumbering.py
@@ -42,7 +42,7 @@ class StandardNumbering(
 
     _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
     _commit: Optional[str] = PrivateAttr(
-        default="ad73396d3a347dd8d413a3cbe77883edb2777380"
+        default="72d2203f2e3ce4b319b29fa0d2f146b5eead7b00"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyeed"
-version = "0.3.5"
+version = "0.3.6"
 description = "Toolkit to create, annotate, and analyze sequence data"
 authors = ["haeussma <[email protected]>"]
 license = "MIT"