# Scoring file suitable for any species with intron sizes similar to mammals
requirements:
  expression: [(cdna_length.multi and (exon_num.multi and min_intron_length and max_intron_length)) or (cdna_length.mono and exon_num.mono))]
  parameters:
    cdna_length.mono: {operator: gt, value: 200}
    cdna_length.multi: {operator: ge, value: 200}
    exon_num.mono: {operator: eq, value: 1}
    exon_num.multi: {operator: gt, value: 1}
    max_intron_length: {operator: le, value: 50000}
    min_intron_length: {operator: ge, value: 5}
cds_requirements:
  expression: [combined_cds_length]
  parameters:
    combined_cds_length: {operator: ge, value: 0}
as_requirements:
  expression: [cdna_length and max_intron_length]
  parameters:
    cdna_length: {operator: ge, value: 200}
#    utr_length: {operator: le, value: 3500}
#    five_utr_length: {operator: le, value: 3500}
#    three_utr_length: {operator: le, value: 3500}
#    suspicious_splicing: {operator: ne, value: true}
    max_intron_length: {operator: le, value: 50000}
#    three_utr_num: {operator: lt, value: 3}
#    five_utr_num: {operator: lt, value: 4}
not_fragmentary:
 expression: [exon_num.multi  or exon_num.mono]
 parameters:
#   is_complete: {operator: eq, value: true}
   exon_num.multi: {operator: gt, value: 1}
#   cdna_length.multi: {operator: ge, value: 400}
#   combined_cds_length.multi: {operator: gt, value: 200}
   exon_num.mono: {operator: eq, value: 1}
#   combined_cds_length.mono: {operator: gt, value: 600}
scoring:
  cdna_length: {rescaling: max}
  exon_num: {
    rescaling: max,
    filter: {
    operator: ge,
    value: 3}
  }
  intron_fraction: {rescaling: max}
  retained_fraction: {rescaling: min}
  retained_intron_num: {rescaling: min}