Source Code for Module Bio.AlignAce.Scanner

 1  # Copyright 2003 by Bartek Wilczynski.  All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5  """ 
 6  Consumers for AlignACE and CompareACE parsers (DEPRECATED). 
 7  """ 
 8   
 9  import warnings 
10  warnings.warn('Bio.AlignAce is deprecated. Please use Bio.Motif instead.', 
11                DeprecationWarning) 
12   
13   
14 -class AlignAceScanner: 
15      """Scannner for AlignACE output 
16   
17      Methods: 
18      feed     Feed data into the scanner. 
19   
20      The scanner generates (and calls the consumer) the following types of events: 
21   
22      noevent - blank line 
23   
24      version - AlignACE version number 
25      command_line - AlignACE command line string 
26      parameters - the begining of the parameters 
27      parameter - the line containing a parameter 
28      sequences - the begining of the sequences list 
29      sequence - line containing the name of the input sequence (and a respective number) 
30      motif - the begining of the motif (contains the number) 
31      motif_hit - one hit for a motif 
32      motif_mask - mask of the motif (space - gap, asterisk - significant position) 
33      motif_score - MAP score of the motif - approx. N * log R, where R == (num. of actual occur.) / (num. of occur. expected by random.) 
34       
35      """ 
36 -    def feed(self, handle, consumer): 
37          """S.feed(handle, consumer) 
38   
39          Feed in a AlignACE report for scanning.  handle is a file-like 
40          object that contains the AlignACE report.  consumer is a Consumer 
41          object that will receive events as the report is scanned. 
42          """ 
43          consumer.version(handle.readline()) 
44          consumer.command_line(handle.readline()) 
45          for line in handle: 
46              if line.strip() == "": 
47                  consumer.noevent(line) 
48              elif line[:4]=="Para": 
49                  consumer.parameters(line) 
50              elif line[0]=="#": 
51                  consumer.sequence(line) 
52              elif "=" in line: 
53                  consumer.parameter(line) 
54              elif line[:5]=="Input": 
55                  consumer.sequences(line) 
56              elif line[:5]=="Motif": 
57                  consumer.motif(line) 
58              elif line[:3]=="MAP": 
59                  consumer.motif_score(line) 
60              elif len(line.split("\t"))==4: 
61                  consumer.motif_hit(line) 
62              elif "*" in line: 
63                  consumer.motif_mask(line) 
64              else: 
65                  raise ValueError(line) 
66   
67 -class CompareAceScanner: 
68      """Scannner for CompareACE output 
69   
70      Methods: 
71      feed     Feed data into the scanner. 
72   
73      The scanner generates (and calls the consumer) the following types of events: 
74   
75      motif_score - CompareACE score of motifs 
76   
77      ###### TO DO #############3 
78      extend the scanner to include other, more complex outputs. 
79      """ 
80 -    def feed(self, handle, consumer): 
81          """S.feed(handle, consumer) 
82   
83          Feed in a CompareACE report for scanning.  handle is a file-like 
84          object that contains the CompareACE report.  consumer is a Consumer 
85          object that will receive events as the report is scanned. 
86          """ 
87          consumer.motif_score(handle.readline()) 
88