Source Code for Module biana.utilities.TsvReader

 1   
 2  from FormattedFileProcessor import FormattedFileProcessor 
 3  import sets 
 4   
 5 -class TsvReader(FormattedFileProcessor): 
 6      """ 
 7          Read/process TSV (tab seperated) formatted files 
 8      """ 
 9 -    def __init__(self, input_file_name): 
10          FormattedFileProcessor.__init__(self, input_file_name=input_file_name, input_type="tsv") 
11          return 
12   
13 -    def process(self, out_method, fields_to_include=None): 
14          """ 
15              Read and process an input file line by line. If out_method is None a dictionary storing read lines are returned. 
16              out_method: method to output columns in current line on the fly in tsv format 
17              fields_to_include: columns that would be included in the dictionary or processed with the function 
18          """ 
19          file = open(self.input_file_name) 
20          line = file.readline() 
21          cols = [ c.lower() for c in line.strip().split('\t') ] 
22          if fields_to_include is None: 
23              first_column = cols[0] 
24          else: 
25              fields_to_include = [ f.lower() for f in fields_to_include ] 
26              first_column = fields_to_include[0] 
27          columns = dict(zip(cols, range(len(cols)))) 
28          id_to_value = {} 
29          i=0 
30          line = file.readline() 
31          while line: 
32              vals = line.strip().split('\t') 
33              if out_method is None: 
34                  if fields_to_include is None: 
35                      id_to_value[vals[columns[first_column]]] = vals 
36                  else: 
37                      id_to_value[vals[columns[first_column]]] = [ vals[columns[f]] for f in fields_to_include] 
38              else: 
39                  out_method("%s\n" % "\t".join([ vals[columns[f]] for f in fields_to_include ])) 
40              i+=1 
41              #if i > 20: 
42              #   break 
43              line = file.readline() 
44          file.close() 
45          if out_method is None: 
46              if fields_to_include is not None: 
47                  cols2 = [] 
48                  for c in cols: 
49                      if c in fields_to_include: 
50                          cols2.append(c) 
51                  columns = dict(zip(cols2, range(len(cols2)))) 
52              return columns, id_to_value 
53          else: 
54              return 
55