riverine.references

riverine.references#

Attributes#

_REF_COLUMNS

_REF_DTYPES

RefFile

_REF_COLUMNS

Classes#

Reference

Functions#

_new_ref_df(→ pandas.DataFrame)

_parse_idt_coa(→ pandas.DataFrame)

load_reference(→ Reference)

Module Contents#

riverine.references._REF_COLUMNS = ['Name', 'Plate', 'Well', 'Concentration (nM)', 'Sequence'][source]#
riverine.references._REF_DTYPES[source]#
type riverine.references.RefFile = 'str | tuple[str, DecimalQuantity | str | dict[str, DecimalQuantity]]'[source]#
riverine.references._new_ref_df() → pandas.DataFrame[source]#
class riverine.references.Reference[source]#
df: pandas.DataFrame[source]#
property loc: pandas.core.indexing._LocIndexer[source]#
__getitem__(key: Any) → Any[source]#
__eq__(other: object) → bool[source]#
__len__() → int[source]#
plate_map(name: str, plate_type: riverine.locations.PlateType = PlateType.wells96) → riverine.mixes.PlateMap[source]#

Return a PlateMap for a given plate name in the Reference.

Parameters:

  • name – Name of plate to make a PlateMap for.

  • plate_type – Either PlateType.wells96 or PlateType.wells384; default is PlateType.wells96.

Returns:

  • a PlateMap consisting of all strands in this Reference object from plate named

  • name. Currently always makes a 96-well plate.

Raises:

ValueError: – If name is not the name of a plate in the reference.

search(name: str | None = None, plate: str | None = None, well: str | riverine.locations.WellPos | None = None, concentration: str | riverine.units.DecimalQuantity | None = None, sequence: str | None = None) → Reference[source]#
get_concentration(name: str | None = None, plate: str | None = None, well: str | riverine.locations.WellPos | None = None, concentration: str | riverine.units.DecimalQuantity | None = None, sequence: str | None = None) → riverine.units.DecimalQuantity[source]#
classmethod from_csv(filename_or_file: str | TextIO | os.PathLike[str]) → Reference[source]#

Load reference information from a CSV file.

The reference information loaded by this function should be compiled manually, fitting the mix reference format, or be loaded with compile_reference() or update_reference().

to_csv(filename: str | os.PathLike[str]) → None[source]#
update(files: Sequence[RefFile] | RefFile, round: int = -1) → Reference[source]#

Update reference information.

This updates an existing reference dataframe with new files, with the same methods as compile_reference().

classmethod compile(files: Sequence[RefFile] | RefFile, round: int = -1) → Reference[source]#

Compile reference information.

This loads information from the following sources:

  • An IDT plate order spreadsheet. This does not include concentration. To add concentration information, list it as a tuple of

(file, concentration). - An IDT bulk order entry text file. - An IDT plate spec sheet.

riverine.references._REF_COLUMNS = ['Name', 'Plate', 'Well', 'Concentration (nM)', 'Sequence'][source]#
riverine.references._parse_idt_coa(df: pandas.DataFrame) → pandas.DataFrame[source]#
riverine.references.load_reference(filename_or_file: str | TextIO) → Reference[source]#