rcx_tk.sequence

Functions

process_sequence_file(→ None)	Processes a metadata file, keeping and renaming specific columns.
process_sequence(→ pandas.DataFrame)	Processes the metadata dataframe.
cleanup(→ pandas.DataFrame)	Removes the file Name column and moves the sampleName col.
validate_injection_order(→ bool)	Validates if injectionOrder is of integer type.
derive_additional_metadata(→ pandas.DataFrame)	Derives additional metadata columns.
rearrange_columns(→ pandas.DataFrame)	Rearranges the columns.
validate_filenames_column(→ None)	Validates the file names.
add_local_order(→ int)	Returns the localOrder value, i.e. the last n-digits after the last underscore.
add_sequence_identifier(→ str)	Returns the sequenceIdentifier value, i.e. everything before last _[digits].
separate_filename(→ Tuple[str, str])	Split a filename into the non-numeric prefix and trailing numeric suffix.
add_subject_identifier(→ str)	Returns the subjectIdentifier value, i.e. everything between [digit_] and [_digit].

Module Contents

rcx_tk.sequence.process_sequence_file(file_path: str, out_path: str) → None

Processes a metadata file, keeping and renaming specific columns.

Parameters:

• file_path (str) – A path to the metadata file.

• out_path (str) – A path where processed metadata dataframe is exported.

rcx_tk.sequence.process_sequence(df: pandas.DataFrame) → pandas.DataFrame

Processes the metadata dataframe.

Parameters:

df (pd.DataFrame) – The metadata dataframe.

Returns:

A metadata dataframe with rearranged and newly derived columns.

Return type:

pd.DataFrame

rcx_tk.sequence.cleanup(df: pandas.DataFrame) → pandas.DataFrame

Removes the file Name column and moves the sampleName col.

Parameters:

df (pd.DataFrame) – The metadata dataframe.

Returns:

The processed dataframe.

Return type:

pd.DataFrame

rcx_tk.sequence.validate_injection_order(df: pandas.DataFrame) → bool

Validates if injectionOrder is of integer type.

Parameters:

df (pd.DataFrame) – The metadata dataframe.

Returns:

Whether the injectionOrder is integer.

Return type:

bool

rcx_tk.sequence.derive_additional_metadata(df: pandas.DataFrame) → pandas.DataFrame

Derives additional metadata columns.

Parameters:

df (pd.DataFrame) – The metadata dataframe.

Returns:

The processed dataframe.

Return type:

pd.DataFrame

rcx_tk.sequence.rearrange_columns(df: pandas.DataFrame) → pandas.DataFrame

Rearranges the columns.

Parameters:

df (pd.DataFrame) – The metadata dataframe.

Returns:

The processed dataframe.

Return type:

pd.DataFrame

rcx_tk.sequence.validate_filenames_column(df: pandas.DataFrame) → None

Validates the file names.

Parameters:

df (pd.DataFrame) – A dataframe to process.

Raises:

ValueError – An error if there is any invalid file name.

rcx_tk.sequence.add_local_order(file_name: str) → int

Returns the localOrder value, i.e. the last n-digits after the last underscore.

Parameters:

file_name (str) – The filename.

Returns:

The localOrder value.

Return type:

int

rcx_tk.sequence.add_sequence_identifier(file_name: str) → str

Returns the sequenceIdentifier value, i.e. everything before last _[digits].

Parameters:

file_name (str) – The filename.

Returns:

The sequenceIdentifier value.

Return type:

str

rcx_tk.sequence.separate_filename(file_name: str) → Tuple[str, str]

Split a filename into the non-numeric prefix and trailing numeric suffix.

Parameters:

file_name (str) – The filename.

Returns:

Splitted file_name.

Return type:

Tuple[str, str]

rcx_tk.sequence.add_subject_identifier(file_name: str) → str

Returns the subjectIdentifier value, i.e. everything between [digit_] and [_digit].

Parameters:

file_name (str) – The filename.

Returns:

The subjectIdentifier value.

Return type:

str