cool-seq-tool 0.4.1__py3-none-any.whl → 0.5.1__py3-none-any.whl

cool_seq_tool/routers/default.py

@@ -1,126 +0,0 @@
-"""Module containing default routes"""
-
-import logging
-import os
-import tempfile
-from pathlib import Path
-
-from fastapi import APIRouter, HTTPException, Query
-from fastapi.responses import FileResponse
-from starlette.background import BackgroundTasks
-
-from cool_seq_tool.routers import (
-    RESP_DESCR,
-    SERVICE_NAME,
-    UNHANDLED_EXCEPTION_MSG,
-    cool_seq_tool,
-)
-from cool_seq_tool.schemas import (
-    GenomicDataResponse,
-    GenomicRequestBody,
-    TranscriptRequestBody,
-)
-from cool_seq_tool.utils import service_meta
-
-logger = logging.getLogger("cool_seq_tool")
-
-router = APIRouter(prefix=f"/{SERVICE_NAME}")
-
-
-@router.post(
-    "/genomic_to_transcript_exon_coordinates",
-    summary="Get transcript exon data given genomic coordinate data",
-    response_description=RESP_DESCR,
-    description="Return transcript exon data",
-    response_model=GenomicDataResponse,
-)
-async def genomic_to_transcript_exon_coordinates(
-    request_body: GenomicRequestBody,
-) -> GenomicDataResponse:
-    """Get transcript exon data given genomic coordinate data
-
-    :param GenomicRequestBody request_body: Request body
-
-    Returns: GenomicDataResponse with data and warnings
-    """
-    request_body = request_body.model_dump()
-
-    response = GenomicDataResponse(
-        genomic_data=None, warnings=[], service_meta=service_meta()
-    )
-
-    try:
-        response = await cool_seq_tool.ex_g_coords_mapper.genomic_to_transcript_exon_coordinates(
-            **request_body
-        )
-    except Exception as e:
-        logger.error("genomic_to_transcript_exon_coordinates unhandled exception %s", e)
-        response.warnings.append(UNHANDLED_EXCEPTION_MSG)
-
-    return response
-
-
-@router.post(
-    "/transcript_to_genomic_coordinates",
-    summary="Get genomic coordinate data given transcript exon data",
-    response_description=RESP_DESCR,
-    description="Return genomic coordinate data",
-    response_model=GenomicDataResponse,
-)
-async def transcript_to_genomic_coordinates(
-    request_body: TranscriptRequestBody,
-) -> GenomicDataResponse:
-    """Get transcript exon data given genomic coordinate data
-
-    :param TranscriptRequestBody request_body: Request body
-
-    Returns: GenomicDataResponse with data and warnings
-    """
-    request_body = request_body.model_dump()
-
-    response = GenomicDataResponse(
-        genomic_data=None, warnings=[], service_meta=service_meta()
-    )
-
-    try:
-        response = (
-            await cool_seq_tool.ex_g_coords_mapper.transcript_to_genomic_coordinates(
-                **request_body
-            )
-        )
-    except Exception as e:
-        logger.error("transcript_to_genomic_coordinates unhandled exception %s", e)
-        response.warnings.append(UNHANDLED_EXCEPTION_MSG)
-
-    return response
-
-
-@router.get(
-    "/download_sequence",
-    summary="Get sequence for ID",
-    response_description=RESP_DESCR,
-    description="Given a known accession identifier, retrieve sequence data and return"
-    "as a FASTA file",
-    response_class=FileResponse,
-)
-async def get_sequence(
-    background_tasks: BackgroundTasks,
-    sequence_id: str = Query(
-        ..., description="ID of sequence to retrieve, sans namespace"
-    ),
-) -> FileResponse:
-    """Get sequence for requested sequence ID.
-    :param sequence_id: accession ID, sans namespace, eg `NM_152263.3`
-    :param background_tasks: Starlette background tasks object. Use to clean up
-        tempfile after get method returns.
-    :return: FASTA file if successful, or 404 if unable to find matching resource
-    """
-    _, path = tempfile.mkstemp(suffix=".fasta")
-    try:
-        cool_seq_tool.seqrepo_access.get_fasta_file(sequence_id, Path(path))
-    except KeyError as e:
-        raise HTTPException(
-            status_code=404, detail="No sequence available for requested identifier"
-        ) from e
-    background_tasks.add_task(lambda p: os.unlink(p), path)  # noqa: PTH108
-    return FileResponse(path)

cool_seq_tool/routers/mane.py

@@ -1,98 +0,0 @@
-"""Module containing routes related to MANE data"""
-
-import logging
-
-from fastapi import APIRouter, Query
-
-from cool_seq_tool.routers import (
-    RESP_DESCR,
-    SERVICE_NAME,
-    UNHANDLED_EXCEPTION_MSG,
-    Tags,
-    cool_seq_tool,
-)
-from cool_seq_tool.schemas import AnnotationLayer, ManeDataService, ResidueMode
-from cool_seq_tool.utils import service_meta
-
-logger = logging.getLogger("cool_seq_tool")
-
-router = APIRouter(prefix=f"/{SERVICE_NAME}/mane")
-
-
-ref_descr = (
-    "Reference at position given during input. When this is set, it will "
-    "ensure that the reference sequences match for the final result."
-)
-try_longest_compatible_descr = (
-    "`True` if should try longest compatible remaining if"
-    " mane transcript was not compatible. `False` otherwise."
-)
-
-
-@router.get(
-    "/get_mane_data",
-    summary="Retrieve MANE data in inter-residue coordinates",
-    response_description=RESP_DESCR,
-    description="Return MANE Select, MANE Plus Clinical, or Longest Remaining "
-    "Transcript data in inter-residue coordinates. See our docs for "
-    "more information on transcript priority.",
-    response_model=ManeDataService,
-    tags=[Tags.MANE_TRANSCRIPT],
-)
-async def get_mane_data(
-    ac: str = Query(..., description="Accession"),
-    start_pos: int = Query(..., description="Start position"),
-    start_annotation_layer: AnnotationLayer = Query(
-        ..., description="Starting annotation layer for query"
-    ),
-    end_pos: int | None = Query(
-        None, description="End position. If not set, will set to `start_pos`."
-    ),
-    gene: str | None = Query(None, description="HGNC gene symbol"),
-    ref: str | None = Query(None, description=ref_descr),
-    try_longest_compatible: bool = Query(
-        True, description=try_longest_compatible_descr
-    ),
-    residue_mode: ResidueMode = Query(
-        ResidueMode.RESIDUE, description="Residue mode for position(s)"
-    ),
-) -> ManeDataService:
-    """Return MANE or Longest Compatible Remaining Transcript data on inter-residue
-    coordinates
-
-    :param str ac: Accession
-    :param int start_pos: Start position
-    :param AnnotationLayer start_annotation_layer: Starting annotation layer for query
-    :param Optional[int] end_pos: End position. If `None` assumes
-        both  `start_pos` and `end_pos` have same values.
-    :param Optional[str] gene: Gene symbol
-    :param Optional[str] ref: Reference at position given during input
-    :param bool try_longest_compatible: `True` if should try longest
-        compatible remaining if mane transcript was not compatible.
-        `False` otherwise.
-    :param ResidueMode residue_mode: Starting residue mode for `start_pos`
-        and `end_pos`. Will always return coordinates in inter-residue
-    """
-    warnings = []
-    mane_data = None
-    try:
-        mane_data = await cool_seq_tool.mane_transcript.get_mane_transcript(
-            ac=ac,
-            start_pos=start_pos,
-            end_pos=end_pos,
-            start_annotation_layer=start_annotation_layer,
-            gene=gene,
-            ref=ref,
-            try_longest_compatible=try_longest_compatible,
-            residue_mode=residue_mode,
-        )
-
-        if not mane_data:
-            warnings.append("Unable to retrieve MANE data")
-    except Exception as e:
-        logger.exception("get_mane_data unhandled exception %s", e)
-        warnings.append(UNHANDLED_EXCEPTION_MSG)
-
-    return ManeDataService(
-        mane_data=mane_data, warnings=warnings, service_meta=service_meta()
-    )

cool_seq_tool/routers/mappings.py

@@ -1,155 +0,0 @@
-"""Module containing routes related to alignment mapping"""
-
-import logging
-
-from fastapi import APIRouter, Query
-
-from cool_seq_tool.routers import RESP_DESCR, SERVICE_NAME, Tags, cool_seq_tool
-from cool_seq_tool.schemas import Assembly, ResidueMode, ToCdnaService, ToGenomicService
-from cool_seq_tool.utils import service_meta
-
-logger = logging.getLogger("cool_seq_tool")
-
-router = APIRouter(prefix=f"/{SERVICE_NAME}/alignment_mapper")
-
-
-@router.get(
-    "/p_to_c",
-    summary="Translate protein representation to cDNA representation",
-    response_description=RESP_DESCR,
-    description="Given protein accession and positions, return associated cDNA "
-    "accession and positions to codon(s)",
-    response_model=ToCdnaService,
-    tags=[Tags.ALIGNMENT_MAPPER],
-)
-async def p_to_c(
-    p_ac: str = Query(..., description="Protein RefSeq accession"),
-    p_start_pos: int = Query(..., description="Protein start position"),
-    p_end_pos: int = Query(..., description="Protein end position"),
-    residue_mode: ResidueMode = Query(
-        ResidueMode.RESIDUE,
-        description="Residue mode for `p_start_pos` and `p_end_pos`",
-    ),
-) -> ToCdnaService:
-    """Translate protein representation to cDNA representation
-
-    :param str p_ac: Protein RefSeq accession
-    :param int p_start_pos: Protein start position
-    :param int p_end_pos: Protein end position
-    :param ResidueMode residue_mode: Residue mode for `p_start_pos` and `p_end_pos`.
-    :return: ToCdnaService containing cDNA representation, warnings, and
-        service meta
-    """
-    try:
-        c_data, w = await cool_seq_tool.alignment_mapper.p_to_c(
-            p_ac, p_start_pos, p_end_pos, residue_mode
-        )
-    except Exception as e:
-        logger.error("Unhandled exception: %s", str(e))
-        w = "Unhandled exception. See logs for more information."
-        c_data = None
-    return ToCdnaService(
-        c_data=c_data, warnings=[w] if w else [], service_meta=service_meta()
-    )
-
-
-@router.get(
-    "/c_to_g",
-    summary="Translate cDNA representation to genomic representation",
-    response_description=RESP_DESCR,
-    description="Given cDNA accession and positions for codon(s), return associated genomic"
-    " accession and positions for a given target genome assembly",
-    response_model=ToGenomicService,
-    tags=[Tags.ALIGNMENT_MAPPER],
-)
-async def c_to_g(
-    c_ac: str = Query(..., description="cDNA RefSeq accession"),
-    c_start_pos: int = Query(..., description="cDNA start position for codon"),
-    c_end_pos: int = Query(..., description="cDNA end position for codon"),
-    cds_start: int | None = Query(
-        None, description="CDS start site. If not provided, this will be computed."
-    ),
-    residue_mode: ResidueMode = Query(
-        ResidueMode.RESIDUE,
-        description="Residue mode for `c_start_pos` and `c_end_pos`",
-    ),
-    target_genome_assembly: Assembly = Query(
-        Assembly.GRCH38, description="Genomic assembly to map to"
-    ),
-) -> ToGenomicService:
-    """Translate cDNA representation to genomic representation
-
-    :param str c_ac: cDNA RefSeq accession
-    :param int c_start_pos: cDNA start position for codon
-    :param int c_end_pos: cDNA end position for codon
-    :param Optional[int] cds_start: CDS start site. If not provided, this will be
-        computed.
-    :param ResidueMode residue_mode: Residue mode for `c_start_pos` and `c_end_pos`.
-    :param Assembly target_genome_assembly: Genome assembly to get genomic data for
-    :return: ToGenomicService containing genomic representation, warnings, and
-        service meta
-    """
-    try:
-        g_data, w = await cool_seq_tool.alignment_mapper.c_to_g(
-            c_ac,
-            c_start_pos,
-            c_end_pos,
-            cds_start=cds_start,
-            residue_mode=residue_mode,
-            target_genome_assembly=target_genome_assembly,
-        )
-    except Exception as e:
-        logger.error("Unhandled exception: %s", str(e))
-        w = "Unhandled exception. See logs for more information."
-        g_data = None
-    return ToGenomicService(
-        g_data=g_data, warnings=[w] if w else [], service_meta=service_meta()
-    )
-
-
-@router.get(
-    "/p_to_g",
-    summary="Translate protein representation to genomic representation",
-    response_description=RESP_DESCR,
-    description="Given protein accession and positions, return associated genomic "
-    "accession and positions for a given target genome assembly",
-    response_model=ToGenomicService,
-    tags=[Tags.ALIGNMENT_MAPPER],
-)
-async def p_to_g(
-    p_ac: str = Query(..., description="Protein RefSeq accession"),
-    p_start_pos: int = Query(..., description="Protein start position"),
-    p_end_pos: int = Query(..., description="Protein end position"),
-    residue_mode: ResidueMode = Query(
-        ResidueMode.RESIDUE,
-        description="Residue mode for `p_start_pos` and `p_end_pos`",
-    ),
-    target_genome_assembly: Assembly = Query(
-        Assembly.GRCH38, description="Genomic assembly to map to"
-    ),
-) -> ToGenomicService:
-    """Translate protein representation to genomic representation
-
-    :param str p_ac: Protein RefSeq accession
-    :param int p_start_pos: Protein start position
-    :param int p_end_pos: Protein end position
-    :param ResidueMode residue_mode: Residue mode for `p_start_pos` and `p_end_pos`.
-    :param Assembly target_genome_assembly: Genome assembly to get genomic data for
-    :return: ToGenomicService containing genomic representation, warnings, and
-        service meta
-    """
-    try:
-        g_data, w = await cool_seq_tool.alignment_mapper.p_to_g(
-            p_ac,
-            p_start_pos,
-            p_end_pos,
-            residue_mode=residue_mode,
-            target_genome_assembly=target_genome_assembly,
-        )
-    except Exception as e:
-        logger.error("Unhandled exception: %s", str(e))
-        w = "Unhandled exception. See logs for more information."
-        g_data = None
-    return ToGenomicService(
-        g_data=g_data, warnings=[w] if w else [], service_meta=service_meta()
-    )

cool_seq_tool/version.py

@@ -1,3 +0,0 @@
-"""Define package version."""
-
-__version__ = "0.4.1"

cool_seq_tool-0.4.1.dist-info/RECORD

@@ -1,29 +0,0 @@
-cool_seq_tool/__init__.py,sha256=BTfkS0bkMtxBL4yGHc4Z7ubmNhdhY2WALfadnk8N1lw,280
-cool_seq_tool/api.py,sha256=AbCmdUVH8ltwqH8k7DiVsHpujMzb6c5pyAKY12iIC0U,1210
-cool_seq_tool/app.py,sha256=5dBmzTf5SeIF90y_ZyI0K6AMSKgchC33eW_ABN6D8_s,4790
-cool_seq_tool/schemas.py,sha256=8xGrP0rAcKLXtZYEe_DJcNp4zapjhN0StRq8uCjoobE,16720
-cool_seq_tool/utils.py,sha256=lckkyFKxMAqG79SYO3p28q6BWgEjlQP7CumE2TDP1zc,1601
-cool_seq_tool/version.py,sha256=hs3N9Wl67casrrQa2sGIAcpcaUySVk4oLE7JffoQuCI,53
-cool_seq_tool/handlers/__init__.py,sha256=KalQ46vX1MO4SJz2SlspKoIRy1n3c3Vp1t4Y2pIfqow,78
-cool_seq_tool/handlers/seqrepo_access.py,sha256=JB3cg7YiV2JKa7ImJXz4WtP9XWShk9qYvhCCrZnBQ6M,8983
-cool_seq_tool/mappers/__init__.py,sha256=SMSf6sPcu7mdQNuJ4Cj1mbOwFUPuMdFSf0noY4XvTxE,262
-cool_seq_tool/mappers/alignment.py,sha256=6Vk4XEar54ivuH8N7oBqa9gUa8E5GjWCI9hC1HCkM18,9552
-cool_seq_tool/mappers/exon_genomic_coords.py,sha256=tOmo6kFGcFIRmLBQwSsIZUSiratiyACf946YKV_IU78,38544
-cool_seq_tool/mappers/mane_transcript.py,sha256=RrVRUS4IqxxX-HyamNLqpQ_WVWABgiLqwmmIh92uny8,49264
-cool_seq_tool/resources/__init__.py,sha256=VwUC8YaucTS6SmRirToulZTF6CuvuLQRSxFfSfAovCc,77
-cool_seq_tool/resources/data_files.py,sha256=3lhu28tzlSoTs4vHZNu-hhoAWRrPGuZj_oIjqk2sYQM,3837
-cool_seq_tool/resources/status.py,sha256=ENsLiwSxzJOLOsY5IKDM805UWbQAOV3w9s7Rv_FLAUs,5761
-cool_seq_tool/resources/transcript_mapping.tsv,sha256=AO3luYQAbFiCoRgiiPXotakb5pAwx1jDCeXpvGdIuac,24138769
-cool_seq_tool/routers/__init__.py,sha256=7SqhLv6_mDPpK1Q0L9aykmjhCmsymFqgbSWZH8LuCW0,437
-cool_seq_tool/routers/default.py,sha256=zqeQmHmfGUvV32xLbN-fUfYnK_UI1gpqIL8Eu5Y8KzY,3928
-cool_seq_tool/routers/mane.py,sha256=boZKP5PH0BAcqEeTBBr9Z3EMY4lhvLLX-pJxUqjBZQ0,3508
-cool_seq_tool/routers/mappings.py,sha256=UJaip0QvRfK3Lk3eVuwofUwg2XJqMV5OVY9OLcpnWS4,6061
-cool_seq_tool/sources/__init__.py,sha256=51QiymeptF7AeVGgV-tW_9f4pIUr0xtYbyzpvHOCneM,304
-cool_seq_tool/sources/mane_transcript_mappings.py,sha256=9Rd_tRCrTk9i9Urp-pMMttq4cCbIJaEJ0n8rM9y9-7I,4077
-cool_seq_tool/sources/transcript_mappings.py,sha256=903RKTMBO2rbKh6iTQ1BEWnY4C7saBFMPw2_4ATuudg,10054
-cool_seq_tool/sources/uta_database.py,sha256=GJHhYbH130YJo9FIRroR8eavlbaziMwI0JVNP8IPGPM,45636
-cool_seq_tool-0.4.1.dist-info/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
-cool_seq_tool-0.4.1.dist-info/METADATA,sha256=CnZwl-rVLfY6kcVkQKYsYziT19q48qHRkYFQ96-OCx0,6262
-cool_seq_tool-0.4.1.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
-cool_seq_tool-0.4.1.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
-cool_seq_tool-0.4.1.dist-info/RECORD,,