Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

86 wrong attribute type in msa #87

Merged
merged 7 commits into from
Jun 21, 2024
Merged

86 wrong attribute type in msa #87

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
03c9802
API update
Jun 21, 2024
071b744
added type annotation for MSA
haeussma Jun 21, 2024
86ab1c4
Merge branch '86-wrong-attribute-type-in-msa' of https://github.com/P…
haeussma Jun 21, 2024
72d2203
bump version
haeussma Jun 21, 2024
60cbcf5
API update
Jun 21, 2024
8a49523
removed api generation
haeussma Jun 21, 2024
cedb79b
Merge branch '86-wrong-attribute-type-in-msa' of https://github.com/P…
haeussma Jun 21, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 0 additions & 14 deletions .github/workflows/generate_api.yaml
View file
Open in desktop

This file was deleted.

27 changes: 21 additions & 6 deletions pyeed/align/msa.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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,
Expand Down Expand Up @@ -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",
Expand All @@ -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()
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/abstractannotation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/alignmentresult.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/blastdata.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/clustalomegaresult.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/dnarecord.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/numberedsequence.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/organism.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/pairwisealignmentresult.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/proteinrecord.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/region.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/regionset.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/sequence.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/sequencerecord.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/site.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyeed/core/standardnumbering.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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 <83341109+haeussma@users.noreply.github.com>"]
license = "MIT"
Expand Down
Loading