latch.verified package

Submodules

latch.verified.deseq2 module

latch.verified.mafft module

class latch.verified.mafft.AlignmentMode(value)

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)

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)

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)

Bases: enum.Enum

An enumeration.

single = 'single'

paired = 'paired'

class latch.verified.rnaseq.Strandedness(value)

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]])

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)

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)

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)

Bases: enum.Enum

An enumeration.

phred33 = '--phred33'

phred64 = '--phred64'

class latch.verified.trim_galore.AdapterSequence(value)

Bases: enum.Enum

An enumeration.

auto = 'auto'

illumina = '--illumina'

stranded_illumina = '--stranded_illumina'

nextera = '--nextera'

small_rna = '--small_rna'

Module contents