1 from logging import debug,root,DEBUG
2
3
4
5 from obitools.word import wordSelector,allWordIterator
6 from obitools.word import predicat
7 import sys
8
9
10
15
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22
23
25
26 optionManager.add_option('-L','--oligo-list',
27 action="store", dest="oligoList",
28 metavar="<filename>",
29 type="str",
30 help="filename containing a list of oligonucleotide")
31
32
33 optionManager.add_option('-s','--oligo-size',
34 action="store", dest="oligoSize",
35 metavar="<###>",
36 type="int",
37 help="Size of oligonucleotide to generate")
38
39 optionManager.add_option('-f','--family-size',
40 action="store", dest="familySize",
41 metavar="<###>",
42 type="int",
43 help="Size of oligonucleotide family to generate")
44
45 optionManager.add_option('-d','--distance',
46 action="store", dest="oligoDist",
47 metavar="<###>",
48 type="int",
49 default=1,
50 help="minimal distance between two oligonucleotides")
51
52 optionManager.add_option('-g','--gc-max',
53 action="store", dest="gcMax",
54 metavar="<###>",
55 type="int",
56 default=0,
57 help="maximum count of G or C nucleotide acceptable in a word")
58
59 optionManager.add_option('-a','--accepted',
60 action="callback", callback=_acceptedOptionCallback,
61 metavar="<regular pattern>",
62 type="str",
63 help="pattern of accepted oligonucleotide")
64
65 optionManager.add_option('-r','--rejected',
66 action="callback", callback=_rejectedOptionCallback,
67 metavar="<regular pattern>",
68 type="str",
69 help="pattern of rejected oligonucleotide")
70
71 optionManager.add_option('-p','--homopolymere',
72 action="store", dest="homopolymere",
73 metavar="<###>",
74 type="int",
75 default=0,
76 help="reject oligo with homopolymere longer than.")
77
78 optionManager.add_option('-P','--homopolymere-min',
79 action="store", dest="homopolymere_min",
80 metavar="<###>",
81 type="int",
82 default=0,
83 help="accept only oligo with homopolymere longer than.")
84
115