How can I insert data from a CSV file into a dataframe using pandas.read_csv?

Question

I have a csv file like:

"B/G/213","B/C/208","WW_cis",,
"B/U/215","B/A/206","WW_cis",,
"B/C/214","B/G/207","WW_cis",,
"B/G/217","B/C/204","WW_cis",,
"B/A/216","B/U/205","WW_cis",,
"B/C/219","B/G/202","WW_cis",,
"B/U/218","B/A/203","WW_cis",,
"B/G/201","B/C/220","WW_cis",,
"B/A/203","B/U/218","WW_cis",,

and I want to read it into something like an array or dataframe, so that I would be able to compare elements from one column to selected elements from another columns. At first, I have read it straight into an array using numpy.genfromtxt, but I got stings like '"B/A/203"' with extra quotes " everywhere. I read somewhere, that pandas allows to strip strings of extra " so I tried:

class StructureReader(object):
    def __init__(self, filename):
        self.filename=filename
    def read(self):
        self.data=pd.read_csv(StringIO(str("RNA/"+self.filename)), header=None, sep = ",")
        self.data

but I get something like so:

<class 'pandas.core.frame.DataFrame'> 0 0 RNA/4v6p.csv

How can I get my CSV file into some kind of a data type that would allow me to search through columns and rows?

Answer 1

Data Insert

You are putting the string of the filename into your DataFrame, i.e. RNA/4v6p.csv is your data in location row 0, col 0. You need to read in the file and store the data. This can be done by removing StringIO(str(...)) in your class

class StructureReader(object):
    def __init__(self, filename):
        self.filename = filename
    def read(self):
        self.data = pd.read_csv("RNA/"+self.filename), header=None, sep = ",")
        self.data

Code structure critique

I would also recommend removing the parent directory from being hardcoded by

1. Always passing in a full file path

   class StructureReader(object):
       def __init__(self, filepath):
           self.filepath = filepath
       def read(self):
           self.data = pd.read_csv(self.filepath), header=None, sep = ",")
           self.data
   

2. Making the directory an __init__() argument

   class StructureReader(object):
       def __init__(self, directory, filename):
           self.directory = directory
           self.filename = filename
       def read(self):
           self.data=pd.read_csv(self.directory+"/"+self.filename), header=None, sep = ",")
           # or import os and self.data=pd.read_csv(os.path.join(self.directory, self.filename)), header=None, sep = ",")
           self.data
   

3. Making the directory a constant attribute

   class StructureReader(object):
       def __init__(self, filename):
           self.directory = "RNA"
           self.filename = filename
       def read(self):
           self.data = pd.read_csv(self.directory+"/"+self.filename), header=None, sep = ",")
           # or import os and self.data=pd.read_csv(os.path.join(self.directory, self.filename)), header=None, sep = ",")
           self.data
   

This has nothing to do with reading your data, just a best practice commentary on structuring you code (Just my $0.02).