Source Code for Module biana.utilities.FormattedFileProcessor

 1  import sets 
 2   
 3 -class FormattedFileProcessor(object): 
 4      """ 
 5          Wrapper around reading/processing various formatted input streams 
 6      """ 
 7      allowed_formats = sets.Set(["sif", "fasta", "tsv"]) 
 8 -    def __init__(self, input_file_name, input_type): 
 9          """ 
10              Initialize an object of this class storing  
11              input_file_name: file name to be read/processed 
12              input_type: could be sif, tsv, fasta, etc.. 
13          """ 
14          self.input_file_name = input_file_name 
15          self.input_type = input_type 
16          if not self.input_type in self.allowed_formats: 
17              raise Exception("Unrecognized input type") 
18          return 
19   
20 -    def read(self, fields_to_include=None): 
21          """ 
22              Read the file into a dictionary and return cloumns names and value dictionary 
23          """ 
24          #raise Exception("Call method of FormattedInputProcesor abstract class") 
25          return self.process(out_method = None, fields_to_include = fields_to_include) 
26   
27 -    def process(self, out_method, fields_to_include): 
28          """ 
29              Read and process an input file line by line. If out_method is None a dictionary storing read lines are returned. 
30              out_method: method to output columns in current line on the fly in the input_type format 
31              fields_to_include: columns that would be included in the dictionary or processed with the function 
32          """ 
33          raise Exception("Call method of FormattedInputProcesor abstract class") 
34          return 
35