# expected data for tests using FBgn0031208.gff and FBgn0031208.gtf files


# list the children and their expected first-order parents for the GFF test file.
GFF_parent_check_level_1 = {
    "FBtr0300690": ["FBgn0031208"],
    "FBtr0300689": ["FBgn0031208"],
    "CG11023:1": ["FBtr0300689", "FBtr0300690"],
    "five_prime_UTR_FBgn0031208:1_737": ["FBtr0300689", "FBtr0300690"],
    "CDS_FBgn0031208:1_737": ["FBtr0300689", "FBtr0300690"],
    "intron_FBgn0031208:1_FBgn0031208:2": ["FBtr0300690"],
    "intron_FBgn0031208:1_FBgn0031208:3": ["FBtr0300689"],
    "FBgn0031208:3": ["FBtr0300689"],
    "CDS_FBgn0031208:3_737": ["FBtr0300689"],
    "CDS_FBgn0031208:2_737": ["FBtr0300690"],
    "exon:chr2L:8193-8589:+": ["FBtr0300690"],
    "intron_FBgn0031208:2_FBgn0031208:4": ["FBtr0300690"],
    "three_prime_UTR_FBgn0031208:3_737": ["FBtr0300689"],
    "FBgn0031208:4": ["FBtr0300690"],
    "CDS_FBgn0031208:4_737": ["FBtr0300690"],
    "three_prime_UTR_FBgn0031208:4_737": ["FBtr0300690"],
}

# and second-level . . . they should all be grandparents of the same gene.
GFF_parent_check_level_2 = {
    "CG11023:1": ["FBgn0031208"],
    "five_prime_UTR_FBgn0031208:1_737": ["FBgn0031208"],
    "CDS_FBgn0031208:1_737": ["FBgn0031208"],
    "intron_FBgn0031208:1_FBgn0031208:2": ["FBgn0031208"],
    "intron_FBgn0031208:1_FBgn0031208:3": ["FBgn0031208"],
    "FBgn0031208:3": ["FBgn0031208"],
    "CDS_FBgn0031208:3_737": ["FBgn0031208"],
    "CDS_FBgn0031208:2_737": ["FBgn0031208"],
    "exon:chr2L:8193-8589:+": ["FBgn0031208"],
    "intron_FBgn0031208:2_FBgn0031208:4": ["FBgn0031208"],
    "three_prime_UTR_FBgn0031208:3_737": ["FBgn0031208"],
    "FBgn0031208:4": ["FBgn0031208"],
    "CDS_FBgn0031208:4_737": ["FBgn0031208"],
    "three_prime_UTR_FBgn0031208:4_737": ["FBgn0031208"],
}

# Same thing for GTF test file . . .
GTF_parent_check_level_1 = {
    "exon:chr2L:7529-8116:+": ["FBtr0300689"],
    "exon:chr2L:7529-8116:+_1": ["FBtr0300690"],
    "exon:chr2L:8193-9484:+": ["FBtr0300689"],
    "exon:chr2L:8193-8589:+": ["FBtr0300690"],
    "exon:chr2L:8668-9484:+": ["FBtr0300690"],
    "exon:chr2L:10000-11000:-": ["transcript_Fk_gene_1"],
    "exon:chr2L:11500-12500:-": ["transcript_Fk_gene_2"],
    "CDS:chr2L:7680-8116:+": ["FBtr0300689"],
    "CDS:chr2L:7680-8116:+_1": ["FBtr0300690"],
    "CDS:chr2L:8193-8610:+": ["FBtr0300689"],
    "CDS:chr2L:8193-8589:+": ["FBtr0300690"],
    "CDS:chr2L:8668-9276:+": ["FBtr0300690"],
    "CDS:chr2L:10000-11000:-": ["transcript_Fk_gene_1"],
    "FBtr0300689": ["FBgn0031208"],
    "FBtr0300690": ["FBgn0031208"],
    "transcript_Fk_gene_1": ["Fk_gene_1"],
    "transcript_Fk_gene_2": ["Fk_gene_2"],
    "start_codon:chr2L:7680-7682:+": ["FBtr0300689"],
    "start_codon:chr2L:7680-7682:+_1": ["FBtr0300690"],
    "start_codon:chr2L:10000-11002:-": ["transcript_Fk_gene_1"],
    "stop_codon:chr2L:8611-8613:+": ["FBtr0300689"],
    "stop_codon:chr2L:9277-9279:+": ["FBtr0300690"],
    "stop_codon:chr2L:11001-11003:-": ["transcript_Fk_gene_1"],
}


GTF_parent_check_level_2 = {
    "exon:chr2L:7529-8116:+": ["FBgn0031208"],
    "exon:chr2L:8193-9484:+": ["FBgn0031208"],
    "exon:chr2L:8193-8589:+": ["FBgn0031208"],
    "exon:chr2L:8668-9484:+": ["FBgn0031208"],
    "exon:chr2L:10000-11000:-": ["Fk_gene_1"],
    "exon:chr2L:11500-12500:-": ["Fk_gene_2"],
    "CDS:chr2L:7680-8116:+": ["FBgn0031208"],
    "CDS:chr2L:8193-8610:+": ["FBgn0031208"],
    "CDS:chr2L:8193-8589:+": ["FBgn0031208"],
    "CDS:chr2L:8668-9276:+": ["FBgn0031208"],
    "CDS:chr2L:10000-11000:-": ["Fk_gene_1"],
    "FBtr0300689": [],
    "FBtr0300690": [],
    "transcript_Fk_gene_1": [],
    "transcript_Fk_gene_2": [],
    "start_codon:chr2L:7680-7682:+": ["FBgn0031208"],
    "start_codon:chr2L:10000-11002:-": ["Fk_gene_1"],
    "stop_codon:chr2L:8611-8613:+": ["FBgn0031208"],
    "stop_codon:chr2L:9277-9279:+": ["FBgn0031208"],
    "stop_codon:chr2L:11001-11003:-": ["Fk_gene_1"],
}

expected_feature_counts = {
    "gff3": {
        "gene": 3,
        "mRNA": 4,
        "exon": 6,
        "CDS": 5,
        "five_prime_UTR": 1,
        "intron": 3,
        "pcr_product": 1,
        "protein": 2,
        "three_prime_UTR": 2,
    },
    "gtf": {
        #'gene':3,
        #   'mRNA':4,
        "CDS": 6,
        "exon": 7,
        "start_codon": 3,
        "stop_codon": 3,
    },
}

expected_features = {
    "gff3": [
        "gene",
        "mRNA",
        "protein",
        "five_prime_UTR",
        "three_prime_UTR",
        "pcr_product",
        "CDS",
        "exon",
        "intron",
    ],
    "gtf": ["gene", "mRNA", "CDS", "exon", "start_codon", "stop_codon"],
}