flybase-cli 0.1.2__py3-none-any.whl

flybase_cli/config.py

@@ -0,0 +1,266 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+
+
+BASE_RELEASES = "https://s3ftp.flybase.org/releases/"
+BASE_API = "https://api.flybase.org/api/v1.0/"
+DEFAULT_RELEASE = "current"
+DEFAULT_ROOT = Path("data/flybase")
+DEFAULT_DB = DEFAULT_ROOT / "flybase.sqlite"
+DEFAULT_MANIFEST = DEFAULT_ROOT / "manifest.json"
+DEFAULT_POSTGRES_DIR = DEFAULT_ROOT / "postgres"
+BATCH_SIZE = 1000
+DELIMITED_SUFFIXES = (".tsv", ".csv", ".tsv.gz", ".csv.gz")
+FASTA_SUFFIXES = (
+    ".fasta",
+    ".fa",
+    ".fna",
+    ".faa",
+    ".fasta.gz",
+    ".fa.gz",
+    ".fna.gz",
+    ".faa.gz",
+)
+GFF_SUFFIXES = (".gff", ".gff3", ".gff.gz", ".gff3.gz")
+GTF_SUFFIXES = (".gtf", ".gtf.gz")
+JSON_SUFFIXES = (".json", ".json.gz")
+INGEST_SUFFIXES = DELIMITED_SUFFIXES + FASTA_SUFFIXES + GFF_SUFFIXES + GTF_SUFFIXES + JSON_SUFFIXES
+SEARCH_ID_CANDIDATES = (
+    "fbgn_id",
+    "primary_fbgn",
+    "flybase_fbgn",
+    "gene_primary_id",
+    "annotation_id",
+    "gene_symbol",
+    "flybase_fbtr",
+    "flybase_fbpp",
+)
+JSON_ID_CANDIDATES = (
+    "primaryId",
+    "primary_id",
+    "id",
+    "fbid",
+    "fbgn_id",
+    "gene_symbol",
+    "symbol",
+    "name",
+)
+JSON_MAX_INFERRED_COLUMNS = 24
+GENOME_SECTIONS = ("fasta", "gff", "gtf", "dna", "chado-xml")
+GENOME_ASSET_PATTERNS = {
+    "mirna": r"miRNA",
+    "transcript": r"transcript",
+    "translation": r"translation",
+    "gene": r"all-gene-",
+    "gene-extended": r"gene_extended2000",
+    "chromosome": r"chromosome",
+    "cds": r"CDS",
+    "ncrna": r"ncRNA",
+    "gff": r"\.gff(\.gz)?$",
+    "gtf": r"\.gtf(\.gz)?$",
+}
+
+
+@dataclass(frozen=True)
+class ManifestSelection:
+    prefix: str
+    includes: tuple[str, ...]
+    excludes: tuple[str, ...] = ()
+
+
+@dataclass(frozen=True)
+class SyncPreset:
+    name: str
+    description: str
+    selections: tuple[ManifestSelection, ...]
+
+    @property
+    def prefixes(self) -> tuple[str, ...]:
+        return tuple(selection.prefix for selection in self.selections)
+
+    @property
+    def includes(self) -> tuple[str, ...]:
+        return tuple(
+            pattern
+            for selection in self.selections
+            for pattern in selection.includes
+        )
+
+    @property
+    def excludes(self) -> tuple[str, ...]:
+        return tuple(
+            pattern
+            for selection in self.selections
+            for pattern in selection.excludes
+        )
+
+
+@dataclass(frozen=True)
+class GenomeSyncPreset:
+    name: str
+    description: str
+    section: str
+    asset: str | None = None
+    includes: tuple[str, ...] = ()
+    excludes: tuple[str, ...] = ()
+
+
+SYNC_PRESETS: dict[str, SyncPreset] = {
+    "gene-core": SyncPreset(
+        name="gene-core",
+        description="Gene summaries plus core identifier/link tables.",
+        selections=(
+            ManifestSelection(
+                prefix="precomputed_files/genes/",
+                includes=(
+                    r"best_gene_summary",
+                    r"fbgn_fbtr_fbpp_fb_",
+                    r"fbgn_annotation_ID",
+                    r"dmel_gene_sequence_ontology_annotations",
+                ),
+            ),
+        ),
+    ),
+    "gene-expression": SyncPreset(
+        name="gene-expression",
+        description="Expression-oriented gene reports.",
+        selections=(
+            ManifestSelection(
+                prefix="precomputed_files/genes/",
+                includes=(
+                    r"curated_expression",
+                    r"high-throughput_gene_expression",
+                    r"gene_rpkm_report",
+                    r"FlyCellAtlas_slimmed_gene_expression",
+                    r"scRNA",
+                ),
+            ),
+        ),
+    ),
+    "references": SyncPreset(
+        name="references",
+        description="Publication and cross-reference tables.",
+        selections=(
+            ManifestSelection(
+                prefix="precomputed_files/references/",
+                includes=(
+                    r"fbrf_pmid_pmcid_doi",
+                    r"entity_publication",
+                    r"representative_publications",
+                ),
+            ),
+        ),
+    ),
+    "gene-knowledge": SyncPreset(
+        name="gene-knowledge",
+        description="Core gene facts plus representative publications and orthology tables.",
+        selections=(
+            ManifestSelection(
+                prefix="precomputed_files/genes/",
+                includes=(
+                    r"best_gene_summary",
+                    r"fbgn_fbtr_fbpp_fb_",
+                    r"fbgn_annotation_ID",
+                    r"dmel_gene_sequence_ontology_annotations",
+                ),
+            ),
+            ManifestSelection(
+                prefix="precomputed_files/references/",
+                includes=(
+                    r"entity_publication",
+                    r"representative_publications",
+                ),
+            ),
+            ManifestSelection(
+                prefix="precomputed_files/orthologs/",
+                includes=(
+                    r"orthologs",
+                    r"paralogs",
+                    r"disease",
+                ),
+            ),
+        ),
+    ),
+    "orthology": SyncPreset(
+        name="orthology",
+        description="Ortholog, paralog, and disease-association support tables.",
+        selections=(
+            ManifestSelection(
+                prefix="precomputed_files/orthologs/",
+                includes=(
+                    r"orthologs",
+                    r"paralogs",
+                    r"disease",
+                ),
+            ),
+        ),
+    ),
+    "interactions": SyncPreset(
+        name="interactions",
+        description="Gene- and allele-level interaction tables.",
+        selections=(
+            ManifestSelection(
+                prefix="precomputed_files/genes/",
+                includes=(r"gene_genetic_interactions",),
+            ),
+            ManifestSelection(
+                prefix="precomputed_files/alleles/",
+                includes=(r"allele_genetic_interactions",),
+            ),
+        ),
+    ),
+}
+
+
+GENOME_SYNC_PRESETS: dict[str, GenomeSyncPreset] = {
+    "mirna-fasta": GenomeSyncPreset(
+        name="mirna-fasta",
+        description="miRNA FASTA sequences for a genome build.",
+        section="fasta",
+        asset="mirna",
+    ),
+    "transcript-fasta": GenomeSyncPreset(
+        name="transcript-fasta",
+        description="Transcript FASTA sequences for a genome build.",
+        section="fasta",
+        asset="transcript",
+    ),
+    "translation-fasta": GenomeSyncPreset(
+        name="translation-fasta",
+        description="Protein translation FASTA sequences for a genome build.",
+        section="fasta",
+        asset="translation",
+    ),
+    "gene-fasta": GenomeSyncPreset(
+        name="gene-fasta",
+        description="Gene FASTA sequences for a genome build.",
+        section="fasta",
+        asset="gene",
+    ),
+    "chromosome-fasta": GenomeSyncPreset(
+        name="chromosome-fasta",
+        description="Chromosome FASTA sequences for a genome build.",
+        section="fasta",
+        asset="chromosome",
+    ),
+    "ncrna-fasta": GenomeSyncPreset(
+        name="ncrna-fasta",
+        description="ncRNA FASTA sequences for a genome build.",
+        section="fasta",
+        asset="ncrna",
+    ),
+    "gff-all": GenomeSyncPreset(
+        name="gff-all",
+        description="Primary GFF annotation file for a genome build.",
+        section="gff",
+        asset="gff",
+    ),
+    "gtf-all": GenomeSyncPreset(
+        name="gtf-all",
+        description="Primary GTF annotation file for a genome build.",
+        section="gtf",
+        asset="gtf",
+    ),
+}