cool-seq-tool 0.4.0.dev3__py3-none-any.whl → 0.5.0__py3-none-any.whl

cool_seq_tool/routers/mappings.py

@@ -1,155 +0,0 @@
-"""Module containing routes related to alignment mapping"""
-import logging
-from typing import Optional
-
-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: Optional[int] = 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

@@ -1,2 +0,0 @@
-"""Define package version."""
-__version__ = "0.4.0-dev3"

cool_seq_tool-0.4.0.dev3.dist-info/RECORD

@@ -1,29 +0,0 @@
-cool_seq_tool/__init__.py,sha256=eBycAZIAJBCf51xQLQYHzvUep1i21LMrzBdRLqfe-Fc,352
-cool_seq_tool/api.py,sha256=3Pc0j0pHMZ_3skTkjDlQpcu_MM6kyNPmBrwm_LrH-rw,1234
-cool_seq_tool/app.py,sha256=MpOImt0cE1g_Y1B3DS18AYffUtHF0JucTTqQuhUPibg,3846
-cool_seq_tool/paths.py,sha256=7EA21Vmf9hvct0z_V4oK0WTWOA2FKY2Tavh4nAUXunk,889
-cool_seq_tool/schemas.py,sha256=Uw5OkC0dPM_RC8ZHNn1wLZBZK_kWAkkQQRrh-zOsJjg,15922
-cool_seq_tool/utils.py,sha256=26y_25V029l-ra3We3z-KQFfgRlcvfl2dQ8XJ1t6yfM,1625
-cool_seq_tool/version.py,sha256=RYDQDTkCd_6WYwrUWOOwYuNLV_rVTLqCFz1unXLvp34,57
-cool_seq_tool/data/__init__.py,sha256=pOdws59_iPOP0V4xqx55PdxCUxHSA5N_Eo5L0oZsafs,63
-cool_seq_tool/data/data_downloads.py,sha256=WaTxeCnifBuif89_lo6hFrmTu2gu8Jy8ndB9crcqvFQ,3869
-cool_seq_tool/data/transcript_mapping.tsv,sha256=AO3luYQAbFiCoRgiiPXotakb5pAwx1jDCeXpvGdIuac,24138769
-cool_seq_tool/handlers/__init__.py,sha256=xDQ84N4ImrUBKwGmrg64yGUMh0ArW-DwjJuTkKrIJL4,77
-cool_seq_tool/handlers/seqrepo_access.py,sha256=XUS4zjguXB7OfLZLnQatWwiYVspu87rk50v1WzENvXE,9029
-cool_seq_tool/mappers/__init__.py,sha256=5aE6IRTG8SwOofFR19QHmK-1n2PaKwEPzFGNE0_HS3s,261
-cool_seq_tool/mappers/alignment.py,sha256=htGb9rJab8dAKcMR62NF0uGc5l4KROrMcMAKfSQhva0,9620
-cool_seq_tool/mappers/exon_genomic_coords.py,sha256=usTOYkXt7HIS1mLtNXms6bqStPJR4GO0R1G47X5xZ8c,38638
-cool_seq_tool/mappers/mane_transcript.py,sha256=XB51pcR5TCtteXS525NgP2S7aRU1gnBtB2ZrSltxM1A,49364
-cool_seq_tool/routers/__init__.py,sha256=x00Dq0LzqYoBPbipmyexLbAMUb7Udx8DozfwT-mJo1E,436
-cool_seq_tool/routers/default.py,sha256=nMDcAAdo-QZugs6k43HnYJCzhorg9nFt0TsdXTckVZU,3927
-cool_seq_tool/routers/mane.py,sha256=fASm7wo4ZjYB5l8G5cu4zqObwf811SxLVCJhbeqC_cY,3544
-cool_seq_tool/routers/mappings.py,sha256=I9hxriBlkv9vQp1l_17L-VxQSUJ9-IyLyqwXGue4axg,6091
-cool_seq_tool/sources/__init__.py,sha256=lERBM8cOqlJhYqz_DwOMV5FsWvMvQMbU1KQBxx_cz6M,303
-cool_seq_tool/sources/mane_transcript_mappings.py,sha256=Oyq7cdUJ2j0isROCkHW-rgtU7LtyFon3DJz6hrEl5cU,3750
-cool_seq_tool/sources/transcript_mappings.py,sha256=_CV71tyge24rr7Kb_rJJQTr9uG1lSU_O-HcC9hIc5OQ,9731
-cool_seq_tool/sources/uta_database.py,sha256=6w1_Dy4aEvRv-4cKBqN9HJqoU1fcpnLNO38a0HEYVuo,44717
-cool_seq_tool-0.4.0.dev3.dist-info/LICENSE,sha256=1jbnPcw_qmlDZyD_E_ebjWwjIvBgOD-1biodvBtSl1U,1072
-cool_seq_tool-0.4.0.dev3.dist-info/METADATA,sha256=GoKAAwPZjiZFcSzGn-Pwk0RnWPwLr5R9wvOre9HunMQ,5720
-cool_seq_tool-0.4.0.dev3.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-cool_seq_tool-0.4.0.dev3.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
-cool_seq_tool-0.4.0.dev3.dist-info/RECORD,,