class ExpressionUnits(SymEnum):
"Units used in expression matrix"
RPM = auto()
RPKM = auto()
FPKM = auto()
TPM = auto()
counts = auto()
class DataCategory(SymEnum):
"""categories of experiments based on data accepted"""
long_only = auto()
short_only = auto()
long_short = auto()
long_genome = auto()
kitchen_sink = auto()
class Sample(SymEnum):
"""LRGASP sample identifier"""
WTC11 = auto()
H1_mix = auto()
ES = auto()
blood = auto()
mouse_simulation = auto()
human_simulation = auto()
class Gencode(SymEnum):
"""LRGASP GENCODE version"""
GENCODE_V38 = auto()
GENCODE_VM27 = auto()
class RefGenome(SymEnum):
"""LRGASP reference genomes"""
GRCh38 = auto()
GRCm39 = auto()
class Repository(SymEnum):
"""Public data repositories"""
SRA = auto()
ENA = auto()
INSDC = auto()
ENC = auto()
class Species(SymEnum):
"""Species identifiers"""
human = auto()
mouse = auto()
manatee = auto()
simulated = auto()
class LibraryPrep(SymEnum):
"""Type of library prep"""
CapTrap = auto()
dRNA = auto()
R2C2 = auto()
cDNA = auto()
class Platform(SymEnum):
"""Simplified sequencing platform, mostly used if figuring out LibraryCategory"""
Illumina = auto()
PacBio = auto()
ONT = auto()
class Platform(SymEnum):
"""Simplified sequencing platform"""
Illumina = auto()
PacBio = auto()
ONT = auto()
class Challenge(SymEnum):
"""Challenge identifiers"""
iso_detect_finished = auto()
iso_quant = auto()
iso_detect_draft = auto()
class ResultFileType(SymEnum):
"type of a submitted data file"
model_gtf = auto()
read_model_map = auto()
expression_matrix = auto()
class ExperimentType(SymEnum):
"type of a experiment, assumed from Challenge type"
model = auto()
expression = auto()
class Sample(SymEnum):
"""LRGASP sample identifier"""
WTC11 = auto()
H1_mix = auto()
ES = auto()
Manatee = auto()
