Module c3covid19.formatting

Classes

class out_formats (*args, **kwargs)

Expand source code

class out_formats:
    def get_output(self, data, output_type, outfile):
        """
        Takes in the following required kwargs:

        - data:
            - Type: List of Dictionaries
        - output_type:
            - Type: String
            - What: The output data or file type
            - Choices:
                - all: A dictionary with all returned data
                - objs: Python object (dict or list) of the returned `objs` or `result`
                - pd: Pandas DF of the returned `objs`
                - np: Numpy Array of the returned `objs`
                - csv: Writes a csv and returns python list of the returned `objs`
                - tab: Writes a tab and returns python list of the returned `objs`
        - outfile:
            - Type: String
            - What: The file path to output to
            - Example: "../my_output"
            - Note: Do not include the file extension
            - Note: Is only used in `csv` and `tab` `output_type`s


        Returns a pandas data frame of the input list
        """
        if output_type=="all":
            return data
        if 'result' in data:
            data=data['result']
        else:
            data=data['objs']
        if output_type=="objs":
            return data
        elif output_type=="pd":
            return self.as_pd(data)
        elif output_type=="np":
            return self.as_np(data)
        elif output_type=="csv":
            return self.as_csv(data, outfile)
        elif output_type=="tab":
            return self.as_tab(data, outfile)

    def as_pd(self, data):
        """
        Takes in the following required kwargs:

        - data:
            - Type: List of Dictionaries || Dictionary

        Returns a pandas data frame of the input list
        """
        return pd.DataFrame(data)

    def as_np(self, data):
        """
        Takes in the following required kwargs:

        - data:
            - Type: List of Dictionaries

        Returns a numpy array of the input list
        """
        return self.as_pd(data).to_numpy()

    def as_csv(self, data, outfile):
        """
        Takes in the following required kwargs:

        - data:
            - Type: List of Dictionaries
        - outfile:
            - Type: String
            - What: The file path to output a csv
            - Example: "../my_output"
            - Note: Do not include the .csv extension

        Generates the specified CSV

        Returns the input data
        """
        self.as_pd(data).to_csv(outfile+'.csv', index=False)
        return data

    def as_tab(self, data, outfile):
        """
        Takes in the following required kwargs:

        - data:
            - Type: List of Dictionaries
        - outfile:
            - Type: String
            - What: The file path to output a tab file
            - Example: "../my_output"
            - Note: Do not include the .tab extension

        Generates the specified TAB file

        Returns the input data
        """
        self.as_pd(data).to_csv(outfile+'.tab', sep='\t', index=False)
        return data

Subclasses

• c3api

Methods

def as_csv(self, data, outfile)

Takes in the following required kwargs:

• data:
  • Type: List of Dictionaries
• outfile:
  • Type: String
  • What: The file path to output a csv
  • Example: "../my_output"
  • Note: Do not include the .csv extension

Generates the specified CSV

Returns the input data

Expand source code

def as_csv(self, data, outfile):
    """
    Takes in the following required kwargs:

    - data:
        - Type: List of Dictionaries
    - outfile:
        - Type: String
        - What: The file path to output a csv
        - Example: "../my_output"
        - Note: Do not include the .csv extension

    Generates the specified CSV

    Returns the input data
    """
    self.as_pd(data).to_csv(outfile+'.csv', index=False)
    return data

def as_np(self, data)

Takes in the following required kwargs:

• data:
  • Type: List of Dictionaries

Returns a numpy array of the input list

Expand source code

def as_np(self, data):
    """
    Takes in the following required kwargs:

    - data:
        - Type: List of Dictionaries

    Returns a numpy array of the input list
    """
    return self.as_pd(data).to_numpy()

def as_pd(self, data)

Takes in the following required kwargs:

• data:
  • Type: List of Dictionaries || Dictionary

Returns a pandas data frame of the input list

Expand source code

def as_pd(self, data):
    """
    Takes in the following required kwargs:

    - data:
        - Type: List of Dictionaries || Dictionary

    Returns a pandas data frame of the input list
    """
    return pd.DataFrame(data)

def as_tab(self, data, outfile)

Takes in the following required kwargs:

• data:
  • Type: List of Dictionaries
• outfile:
  • Type: String
  • What: The file path to output a tab file
  • Example: "../my_output"
  • Note: Do not include the .tab extension

Generates the specified TAB file

Returns the input data

Expand source code

def as_tab(self, data, outfile):
    """
    Takes in the following required kwargs:

    - data:
        - Type: List of Dictionaries
    - outfile:
        - Type: String
        - What: The file path to output a tab file
        - Example: "../my_output"
        - Note: Do not include the .tab extension

    Generates the specified TAB file

    Returns the input data
    """
    self.as_pd(data).to_csv(outfile+'.tab', sep='\t', index=False)
    return data

def get_output(self, data, output_type, outfile)

Takes in the following required kwargs:

• data:
  • Type: List of Dictionaries
• output_type:
  • Type: String
  • What: The output data or file type
  • Choices:
    • all: A dictionary with all returned data
    • objs: Python object (dict or list) of the returned objs or result
    • pd: Pandas DF of the returned objs
    • np: Numpy Array of the returned objs
    • csv: Writes a csv and returns python list of the returned objs
    • tab: Writes a tab and returns python list of the returned objs
• outfile:
  • Type: String
  • What: The file path to output to
  • Example: "../my_output"
  • Note: Do not include the file extension
  • Note: Is only used in csv and tab output_types

Returns a pandas data frame of the input list

Expand source code

def get_output(self, data, output_type, outfile):
    """
    Takes in the following required kwargs:

    - data:
        - Type: List of Dictionaries
    - output_type:
        - Type: String
        - What: The output data or file type
        - Choices:
            - all: A dictionary with all returned data
            - objs: Python object (dict or list) of the returned `objs` or `result`
            - pd: Pandas DF of the returned `objs`
            - np: Numpy Array of the returned `objs`
            - csv: Writes a csv and returns python list of the returned `objs`
            - tab: Writes a tab and returns python list of the returned `objs`
    - outfile:
        - Type: String
        - What: The file path to output to
        - Example: "../my_output"
        - Note: Do not include the file extension
        - Note: Is only used in `csv` and `tab` `output_type`s


    Returns a pandas data frame of the input list
    """
    if output_type=="all":
        return data
    if 'result' in data:
        data=data['result']
    else:
        data=data['objs']
    if output_type=="objs":
        return data
    elif output_type=="pd":
        return self.as_pd(data)
    elif output_type=="np":
        return self.as_np(data)
    elif output_type=="csv":
        return self.as_csv(data, outfile)
    elif output_type=="tab":
        return self.as_tab(data, outfile)