Source code for pml.data.loader

# Copyright (C) 2012 David Rusk
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"""
Utilities for loading data sets.

@author: drusk
"""

import os.path

import pandas as pd

from pml.data import model
from pml.interactive import util as shell_util

def load(path, has_ids=True, has_header=True, has_labels=True, delimiter=","):
    """
    Loads a data set from a delimited text file.
    
    Args:
      path: 
        the path to the file containing the data set.
      has_ids: boolean
        set to False if the first column in the loaded dataset should not be 
        interpreted as a feature instead of sample identifiers.  Defaults to 
        True, i.e. first column are interpreted as sample identifiers.
      has_header: boolean
        set to False if the data being loaded does not have column headers on 
        the first line.  Defaults to true.
      has_labels: boolean
        set to False if the data being loaded does not have classification 
        labels for each sample.  Defaults to True.  The labels should be the 
        last column in the dataset being loaded.
      delimiter: string
        the symbol used to separate columns in the file.  Default value is 
        ','.  Hint: delimiter for tab-delimited files is '\t'.
      
    Returns:
      A DataSet object.
    """
    header = 0 if has_header else None
    id_col = 0 if has_ids else None

    dataframe = pd.read_csv(path, index_col=id_col, header=header, 
                            delimiter=delimiter)
    
    labels = dataframe.pop(dataframe.columns[-1]) if has_labels else None

    return model.DataSet(dataframe, labels=labels)

def shell_load(path, has_ids=True, has_header=True, has_labels=True, delimiter=","):
    """
    Loads a data set from a delimited text file.  Will search through sample 
    data sets.
    
    Args:
      path: 
        the path to the file containing the data set.
      has_ids: boolean
        set to False if the first column in the loaded dataset should not be 
        interpreted as a feature instead of sample identifiers.  Defaults to 
        True, i.e. first column are interpreted as sample identifiers.
      has_header: boolean
        set to False if the data being loaded does not have column headers on 
        the first line.  Defaults to true.
      has_labels: boolean
        set to False if the data being loaded does not have classification 
        labels for each sample.  Defaults to True.  The labels should be the 
        last column in the dataset being loaded.
      delimiter: string
        the symbol used to separate columns in the file.  Default value is 
        ','.  Hint: delimiter for tab-delimited files is '\t'.
      
    Returns:
      A DataSet object.
    """
    if path in shell_util.list_samples():
        path = os.path.join(shell_util.get_samples_basepath(), path)
    
    return load(path, has_ids=has_ids, has_header=has_header, 
                has_labels=has_labels, delimiter=delimiter)