latch.verified package#

Submodules#

latch.verified.deseq2 module#

latch.verified.mafft module#

class latch.verified.mafft.AlignmentMode(value)[source]#

Bases: enum.Enum

An enumeration.

linsi = 'L-INS-i'#
fftns2 = 'FFT-NS-2'#
auto = 'auto'#

latch.verified.pathway module#

latch.verified.rnaseq module#

class latch.verified.rnaseq.SingleEndReads(r1: latch.types.file.LatchFile)[source]#

Bases: object

r1: latch.types.file.LatchFile#
classmethod from_dict(kvs: Optional[Union[dict, list, str, int, float, bool]], *, infer_missing=False) dataclasses_json.api.A#
classmethod from_json(s: Union[str, bytes, bytearray], *, parse_float=None, parse_int=None, parse_constant=None, infer_missing=False, **kw) dataclasses_json.api.A#
classmethod schema(*, infer_missing: bool = False, only=None, exclude=(), many: bool = False, context=None, load_only=(), dump_only=(), partial: bool = False, unknown=None) dataclasses_json.mm.SchemaF[dataclasses_json.mm.A]#
to_dict(encode_json=False) Dict[str, Optional[Union[dict, list, str, int, float, bool]]]#
to_json(*, skipkeys: bool = False, ensure_ascii: bool = True, check_circular: bool = True, allow_nan: bool = True, indent: Optional[Union[int, str]] = None, separators: Optional[Tuple[str, str]] = None, default: Optional[Callable] = None, sort_keys: bool = False, **kw) str#
class latch.verified.rnaseq.PairedEndReads(r1: latch.types.file.LatchFile, r2: latch.types.file.LatchFile)[source]#

Bases: object

r1: latch.types.file.LatchFile#
r2: latch.types.file.LatchFile#
classmethod from_dict(kvs: Optional[Union[dict, list, str, int, float, bool]], *, infer_missing=False) dataclasses_json.api.A#
classmethod from_json(s: Union[str, bytes, bytearray], *, parse_float=None, parse_int=None, parse_constant=None, infer_missing=False, **kw) dataclasses_json.api.A#
classmethod schema(*, infer_missing: bool = False, only=None, exclude=(), many: bool = False, context=None, load_only=(), dump_only=(), partial: bool = False, unknown=None) dataclasses_json.mm.SchemaF[dataclasses_json.mm.A]#
to_dict(encode_json=False) Dict[str, Optional[Union[dict, list, str, int, float, bool]]]#
to_json(*, skipkeys: bool = False, ensure_ascii: bool = True, check_circular: bool = True, allow_nan: bool = True, indent: Optional[Union[int, str]] = None, separators: Optional[Tuple[str, str]] = None, default: Optional[Callable] = None, sort_keys: bool = False, **kw) str#
class latch.verified.rnaseq.ReadType(value)[source]#

Bases: enum.Enum

An enumeration.

single = 'single'#
paired = 'paired'#
class latch.verified.rnaseq.Strandedness(value)[source]#

Bases: enum.Enum

An enumeration.

auto = 'auto'#
class latch.verified.rnaseq.Sample(name: str, strandedness: latch.verified.rnaseq.Strandedness, replicates: List[Union[latch.verified.rnaseq.SingleEndReads, latch.verified.rnaseq.PairedEndReads]])[source]#

Bases: object

name: str#
strandedness: latch.verified.rnaseq.Strandedness#
replicates: List[Union[latch.verified.rnaseq.SingleEndReads, latch.verified.rnaseq.PairedEndReads]]#
classmethod from_dict(kvs: Optional[Union[dict, list, str, int, float, bool]], *, infer_missing=False) dataclasses_json.api.A#
classmethod from_json(s: Union[str, bytes, bytearray], *, parse_float=None, parse_int=None, parse_constant=None, infer_missing=False, **kw) dataclasses_json.api.A#
classmethod schema(*, infer_missing: bool = False, only=None, exclude=(), many: bool = False, context=None, load_only=(), dump_only=(), partial: bool = False, unknown=None) dataclasses_json.mm.SchemaF[dataclasses_json.mm.A]#
to_dict(encode_json=False) Dict[str, Optional[Union[dict, list, str, int, float, bool]]]#
to_json(*, skipkeys: bool = False, ensure_ascii: bool = True, check_circular: bool = True, allow_nan: bool = True, indent: Optional[Union[int, str]] = None, separators: Optional[Tuple[str, str]] = None, default: Optional[Callable] = None, sort_keys: bool = False, **kw) str#
class latch.verified.rnaseq.LatchGenome(value)[source]#

Bases: enum.Enum

An enumeration.

RefSeq_hg38_p14 = 'Homo sapiens (RefSeq hg38.p14)'#
RefSeq_T2T_CHM13v2_0 = 'Homo sapiens (RefSeq T2T-CHM13v2.0)'#
RefSeq_R64 = 'Saccharomyces cerevisiae (RefSeq R64)'#
RefSeq_GRCm39 = 'Mus musculus (RefSeq GRCm39)'#
class latch.verified.rnaseq.AlignmentTools(value)[source]#

Bases: enum.Enum

An enumeration.

star_salmon = 'Traditional Alignment + Quantification'#
salmon = 'Selective Alignment + Quantification'#

latch.verified.trim_galore module#

class latch.verified.trim_galore.BaseQualityEncoding(value)[source]#

Bases: enum.Enum

An enumeration.

phred33 = '--phred33'#
phred64 = '--phred64'#
class latch.verified.trim_galore.AdapterSequence(value)[source]#

Bases: enum.Enum

An enumeration.

auto = 'auto'#
illumina = '--illumina'#
stranded_illumina = '--stranded_illumina'#
nextera = '--nextera'#
small_rna = '--small_rna'#

Module contents#