latch.verified package#

Submodules#

latch.verified.deseq2 module#

latch.verified.mafft module#

class latch.verified.mafft.AlignmentMode(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: Enum

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: LatchFile#
classmethod from_dict(kvs: dict | list | str | int | float | bool | None, *, infer_missing=False) → A#
classmethod from_json(s: str | bytes | bytearray, *, parse_float=None, parse_int=None, parse_constant=None, infer_missing=False, **kw) → A#
classmethod schema(*, infer_missing: bool = False, only=None, exclude=(), many: bool = False, context=None, load_only=(), dump_only=(), partial: bool = False, unknown=None) → SchemaF[A]#
to_dict(encode_json=False) → Dict[str, dict | list | str | int | float | bool | None]#
to_json(*, skipkeys: bool = False, ensure_ascii: bool = True, check_circular: bool = True, allow_nan: bool = True, indent: int | str | None = None, separators: Tuple[str, str] = None, default: 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: LatchFile#
r2: LatchFile#
classmethod from_dict(kvs: dict | list | str | int | float | bool | None, *, infer_missing=False) → A#
classmethod from_json(s: str | bytes | bytearray, *, parse_float=None, parse_int=None, parse_constant=None, infer_missing=False, **kw) → A#
classmethod schema(*, infer_missing: bool = False, only=None, exclude=(), many: bool = False, context=None, load_only=(), dump_only=(), partial: bool = False, unknown=None) → SchemaF[A]#
to_dict(encode_json=False) → Dict[str, dict | list | str | int | float | bool | None]#
to_json(*, skipkeys: bool = False, ensure_ascii: bool = True, check_circular: bool = True, allow_nan: bool = True, indent: int | str | None = None, separators: Tuple[str, str] = None, default: Callable = None, sort_keys: bool = False, **kw) → str#
class latch.verified.rnaseq.ReadType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: Enum

single = 'single'#
paired = 'paired'#
class latch.verified.rnaseq.Strandedness(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: Enum

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

Bases: object

name: str#
strandedness: Strandedness#
replicates: List[SingleEndReads | PairedEndReads]#
classmethod from_dict(kvs: dict | list | str | int | float | bool | None, *, infer_missing=False) → A#
classmethod from_json(s: str | bytes | bytearray, *, parse_float=None, parse_int=None, parse_constant=None, infer_missing=False, **kw) → A#
classmethod schema(*, infer_missing: bool = False, only=None, exclude=(), many: bool = False, context=None, load_only=(), dump_only=(), partial: bool = False, unknown=None) → SchemaF[A]#
to_dict(encode_json=False) → Dict[str, dict | list | str | int | float | bool | None]#
to_json(*, skipkeys: bool = False, ensure_ascii: bool = True, check_circular: bool = True, allow_nan: bool = True, indent: int | str | None = None, separators: Tuple[str, str] = None, default: Callable = None, sort_keys: bool = False, **kw) → str#
class latch.verified.rnaseq.LatchGenome(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: Enum

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, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: Enum

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

latch.verified.trim_galore module#

class latch.verified.trim_galore.BaseQualityEncoding(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: Enum

phred33 = '--phred33'#
phred64 = '--phred64'#
class latch.verified.trim_galore.AdapterSequence(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: Enum

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

Module contents#