"""
Field names for various genomic tabular files

"""

__all__ = ["SCHEMAS"]


# UCSC File Formats
# https://genome.ucsc.edu/FAQ/FAQformat.html
BED12_FIELDS = [
    "chrom",
    "start",
    "end",
    "name",
    "score",
    "strand",
    "thickStart",
    "thickEnd",
    "itemRgb",
    "blockCount",
    "blockSizes",
    "blockStarts",
]

BED_FIELDS = BED12_FIELDS[:6]

BEDGRAPH_FIELDS = ["chrom", "start", "end", "value"]

BEDPE_FIELDS = [
    "chrom1",
    "start1",
    "end1",
    "chrom2",
    "start2",
    "end2",
    "name",
    "score",
    "strand1",
    "strand2",
]

GFF_FIELDS = [
    "chrom",
    "source",
    "feature",
    "start",
    "end",
    "score",
    "strand",
    "frame",
    "attributes",
]

PGSNP_FIELDS = [
    "chrom",
    "start",
    "end",
    "name",
    "alleleCount",
    "alleleFreq",
    "alleleScores",
]

BEDRNAELEMENTS_FIELDS = [
    "chrom",
    "start",
    "end",
    "name",
    "score",
    "strand",
    "level",
    "signif",
    "score2",
]

NARROWPEAK_FIELDS = [
    "chrom",
    "start",
    "end",
    "name",
    "score",
    "strand",
    "fc",
    "-log10p",
    "-log10q",
    "relSummit",
]

BROADPEAK_FIELDS = [
    "chrom",
    "start",
    "end",
    "name",
    "score",
    "strand",
    "fc",
    "-log10p",
    "-log10q",
]

GAPPEDPEAK_FIELDS = [
    "chrom",
    "start",
    "end",
    "name",
    "score",
    "strand",
    "thickStart",
    "thickEnd",
    "itemRgb",
    "blockCount",
    "blockSizes",
    "blockStarts",
    "fc",
    "-log10p",
    "-log10q",
]

JASPAR_FIELDS = ["chrom", "start", "end", "name", "score", "pval", "strand"]

GAP_FIELDS = ["bin", "chrom", "start", "end", "ix", "n", "length", "type", "bridge"]

CENTROMERES_FIELDS = ["bin", "chrom", "start", "end", "name"]

UCSC_MRNA_FIELDS = [
    "bin",
    "matches",
    "misMatches",
    "repMatches",
    "nCount",
    "qNumInsert",
    "qBaseInsert",
    "tNumInsert",
    "tBaseInsert",
    "strand",
    "qName",
    "qSize",
    "qStart",
    "qEnd",
    "tName",
    "tSize",
    "tStart",
    "tEnd",
    "blockCount",
    "blockSizes",
    "qStarts",
    "tStarts",
]

CYTOBAND_FIELDS = ["chrom", "start", "end", "name", "gieStain"]


# GA4GH File Formats
# http://ga4gh.org/#/fileformats-team
BAM_FIELDS = [
    "QNAME",
    "FLAG",
    "RNAME",
    "POS",
    "MAPQ",
    "CIGAR",
    "RNEXT",
    "PNEXT",
    "TLEN",
    "SEQ",
    "QUAL",
    "TAGs",
]

VCF_FIELDS = ["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"]


SCHEMAS = {
    "bed": BED_FIELDS,
    "bed3": BED_FIELDS[:3],
    "bed4": BED_FIELDS[:4],
    "bedGraph": BEDGRAPH_FIELDS,
    "bed5": BED_FIELDS[:5],
    "bed6": BED_FIELDS,
    "bed9": BED12_FIELDS[:9],
    "bed12": BED12_FIELDS,
    "bedpe": BEDPE_FIELDS,
    "gff": GFF_FIELDS,
    "gtf": GFF_FIELDS,
    "bedRnaElements": BEDRNAELEMENTS_FIELDS,
    "narrowPeak": NARROWPEAK_FIELDS,
    "broadPeak": BROADPEAK_FIELDS,
    "gappedPeak": GAPPEDPEAK_FIELDS,
    "centromeres": CENTROMERES_FIELDS,
    "cytoband": CYTOBAND_FIELDS,
    "sam": BAM_FIELDS,
    "vcf": VCF_FIELDS,
    "jaspar": JASPAR_FIELDS,
    "gap": GAP_FIELDS,
    "all_mrna": UCSC_MRNA_FIELDS,
    "pgsnp": PGSNP_FIELDS,
}


CHROM_NAME_PATTERNS = {
    "hg19": (
        r"^chr[0-9]+$",
        r"^chr[XY]$",
        r"^chrM$",
        r"^chr(?!Un).+_.*_random$",
        r"^chrUn_.*$",
        r"^chr(?!Un).+_.*_hap\d+$",
    ),
    "hg38": (
        r"^chr[0-9]+$",
        r"^chr[XY]$",
        r"^chrM$",
        r"^chrEBV$",
        r"^chr(?!Un).+_.*_random$",
        r"^chrUn_.*$",
        r"^chr(?!Un).+_.*_alt$",
    ),
    "mm9": (
        r"^chr[0-9]+$",
        r"^chr[XY]$",
        r"^chrM$",
        r"^chr(?!Un).+_random$",
        r"^chrUn_random$",
    ),
    "mm10": (
        r"^chr[0-9]+$",
        r"^chr[XY]$",
        r"^chrM$",
        r"^chr(?!Un).+_random$",
        r"^chrUn_.*$",
    ),
    "galGal4": (
        r"^chr[0-9]+$",
        r"^chr[ZW]$",
        r"^chrM$",
        r"^chrLGE64|chrLGE22C19W28_E50C23$",
        r"^chr(?!Un).+_random$",
        r"^chrUn_.*$",
    ),
    "galGal5": (
        r"^chr[0-9]+$",
        r"^chr[ZW]$",
        r"^chrM$",
        r"^chrLGE64$",
        r"^chr(?!Un).+_random$",
        r"^chrUn_.*$",
    ),
    "dm3": (
        r"^chr[234][LR[Het]*]*$",
        r"^chr[XY][Het]*$",
        r"^chrM$",
        r"^chr[U][extra]*$",
    ),
    "dm6": (
        r"^chr[234][LR]*",
        r"^chr[XY]$",
        r"^chrM$",
        r"^chr(?!Un).+_random$",
        r"^chrUn_.*$",
    ),
    "ce10": (r"chr[IV]+$", r"^chrX$", r"^chrM$"),
    "ce11": (r"chr[IV]+$", r"^chrX$", r"^chrM$"),
    "sacCer3": (r"chr[IXV]+$", r"^chrM$"),
    "TAIR10": (r"^\d+", r"^MT|Pltd$"),
}


UCSC_AUTOSOMES = r"^chr[0-9]+[A-Za-z]*$"
UCSC_SEXCHROMS = r"^chr[XYZW][A-Za-z]*$"
UCSC_NONNUCLEAR = r"^chrM$"
UCSC_OTHER = r"^chrLGE.*$"
UCSC_UNLOCALIZED = r"^chr(?!Un).+.*_random$"
UCSC_UNPLACED = r"^chrUn_.*$|^chrU[A-Za-z]*$"
UCSC_ALTCHROMS = r"^chr(?!Un).+_.*_hap\d+$|^chr(?!Un).+_.*_alt$"
NCBI_AUTOSOMES = r"^[0-9]+$"
NCBI_SEXCHROMS = r"^[XYZW]$"
NCBI_NONNUCLEAR = r"^MT$|^Pltd$"
ROMAN_LT10 = [r"^chrI+$", r"^chrIV$", r"^chrVI*$", r"^chrIX$"]
ROMAN_LT20 = [*ROMAN_LT10, "^chrX$", "^chrXI*$", "^chrXIV$", "^chrXVI*$", "^chrXIX$"]