|
18
|
1 # Copyright INRA (Institut National de la Recherche Agronomique)
|
|
|
2 # http://www.inra.fr
|
|
|
3 # http://urgi.versailles.inra.fr
|
|
|
4 #
|
|
|
5 # This software is governed by the CeCILL license under French law and
|
|
|
6 # abiding by the rules of distribution of free software. You can use,
|
|
|
7 # modify and/ or redistribute the software under the terms of the CeCILL
|
|
|
8 # license as circulated by CEA, CNRS and INRIA at the following URL
|
|
|
9 # "http://www.cecill.info".
|
|
|
10 #
|
|
|
11 # As a counterpart to the access to the source code and rights to copy,
|
|
|
12 # modify and redistribute granted by the license, users are provided only
|
|
|
13 # with a limited warranty and the software's author, the holder of the
|
|
|
14 # economic rights, and the successive licensors have only limited
|
|
|
15 # liability.
|
|
|
16 #
|
|
|
17 # In this respect, the user's attention is drawn to the risks associated
|
|
|
18 # with loading, using, modifying and/or developing or reproducing the
|
|
|
19 # software by the user in light of its specific status of free software,
|
|
|
20 # that may mean that it is complicated to manipulate, and that also
|
|
|
21 # therefore means that it is reserved for developers and experienced
|
|
|
22 # professionals having in-depth computer knowledge. Users are therefore
|
|
|
23 # encouraged to load and test the software's suitability as regards their
|
|
|
24 # requirements in conditions enabling the security of their systems and/or
|
|
|
25 # data to be ensured and, more generally, to use and operate it in the
|
|
|
26 # same conditions as regards security.
|
|
|
27 #
|
|
|
28 # The fact that you are presently reading this means that you have had
|
|
|
29 # knowledge of the CeCILL license and that you accept its terms.
|
|
|
30
|
|
|
31
|
|
|
32 ## @mainpage Documentation of the REPET API
|
|
|
33 #
|
|
|
34 # Welcome to the API documentation!
|
|
|
35 # This API is a set of packages and classes for pipeline(s) development.
|
|
|
36 #
|
|
|
37 # @par The "logger" package
|
|
|
38 #
|
|
|
39 # Logging is managed via LoggerFactory. This class creates instances of logging.logging python class. It's strongly encouraged to use this factory each time you need to log something.
|
|
|
40 #
|
|
|
41 # @par The "checker" package
|
|
|
42 #
|
|
|
43 # This package is a set of classes designed to facilitate development of different kind of checks: filesystem checks, environment checks, configuration file checks ...
|
|
|
44 #
|
|
|
45 # Classes should subclass checker::IChecker or if a logger is needed: checker::AbstractChecker.
|
|
|
46 #
|
|
|
47 # Methods should raise checker::CheckerException.
|
|
|
48 #
|
|
|
49 # Use checker::ConfigChecker and checker::ConfigException for configuration files checks.
|
|
|
50 #
|
|
|
51 # checker::CheckerUtils is a set of small static methods shared by other classes of checker package.
|
|
|
52 #
|
|
|
53 # @par The "coord" package
|
|
|
54 #
|
|
|
55 # This package is a set of classes dedicated to coordinates manipulations.
|
|
|
56 #
|
|
|
57 # A coord::Range instance records a region on a given sequence (start, end and sequence name).
|
|
|
58 #
|
|
|
59 # A coord::Map instance is a coord::Range instance and record a named region on a given sequence (start, end, sequence name and name).
|
|
|
60 #
|
|
|
61 # A coord::Set instance is a coord::Map instance and record a named region on a given sequence with an identifier (start, end, sequence name, name and id).
|
|
|
62 #
|
|
|
63 # A coord::Align instance handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity).
|
|
|
64 #
|
|
|
65 # A coord::Path instance is a coord::Align instance and handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity) with an identifier.
|
|
|
66 #
|
|
|
67 # A coord::Match instance is a coord::Path instance and handle a chain of match(es) between two sequences, query and subject, with an identifier and the length of the input sequences.
|
|
|
68 #
|
|
|
69 # coord::Align, coord::Map, coord::Path and coord::Set come with utils classes: coord::AlignUtils, coord::MapUtils, coord::PathUtils and coord::SetUtils.
|
|
|
70 #
|
|
|
71 # @par The "seq" package
|
|
|
72 #
|
|
|
73 # This package a set of classes dedicated to sequences manipulations.
|
|
|
74 #
|
|
|
75 # A seq::Bioseq instance records a sequence with its header. seq::Bioseq comes with an utils class: seq::BioseqUtils.
|
|
|
76 #
|
|
|
77 # A seq::BioseqDB instance handle a collection of a Bioseq (header-sequence).
|
|
|
78 #
|
|
|
79 # A seq::AlignedBioseqDB instance is a multiple sequence alignment representation.
|
|
|
80 #
|
|
|
81 # A seq::FastaUtils is a set of static methods for fasta file manipulation.
|
|
|
82 #
|
|
|
83 # @par The "sql" package
|
|
|
84 #
|
|
|
85 # This package is dedicated to persistance of coord package objects.
|
|
|
86 # All classes come with dedicated interfaces. Use these interfaces for class manipulation.
|
|
|
87 # Class names patterns are ITable*Adaptator and Table*Adaptator.
|
|
|
88 #
|
|
|
89 # sql::ITablePathAdaptator, sql::TablePathAdaptator /
|
|
|
90 # sql::ITableSetAdaptator, sql::TableSetAdaptator /
|
|
|
91 # sql::ITableSeqAdaptator, sql::TableSeqAdaptator /
|
|
|
92 # sql::ITableMapAdaptator, sql::TableMapAdaptator /
|
|
|
93 # sql::ITableMatchAdaptator, sql::TableMatchAdaptator.
|
|
|
94 #
|
|
|
95
|
|
|
96 import logging
|
|
|
97 import sys
|
|
|
98
|
|
|
99 DEFAULT_LEVEL = 1
|
|
|
100 DEFAULT_FORMAT = "%(asctime)s - %(module)s - %(levelname)s - %(message)s"
|
|
|
101 DATE_FORMAT = "%Y-%m-%d %H:%M:%S"
|
|
|
102
|
|
|
103 ## Use this class to create a instance of logging class.
|
|
|
104 #
|
|
|
105 class LoggerFactory(object):
|
|
|
106
|
|
|
107 def createLogger(name, verbosity = DEFAULT_LEVEL, format = DEFAULT_FORMAT, out = sys.stdout):
|
|
|
108 log = logging.getLogger(name)
|
|
|
109
|
|
|
110 hasStreamHandler = False
|
|
|
111 for handler in log.handlers:
|
|
|
112 if handler.__class__ == logging.StreamHandler:
|
|
|
113 hasStreamHandler = True
|
|
|
114 break
|
|
|
115 if not hasStreamHandler:
|
|
|
116 formatter = logging.Formatter(format, DATE_FORMAT)
|
|
|
117 handler = logging.StreamHandler(out)
|
|
|
118 handler.setFormatter(formatter)
|
|
|
119 log.addHandler(handler)
|
|
|
120
|
|
|
121 LoggerFactory.setLevel(log, verbosity)
|
|
|
122 return log
|
|
|
123
|
|
|
124 createLogger = staticmethod(createLogger)
|
|
|
125
|
|
|
126 def setLevel(log, verbosity):
|
|
|
127 log.disabled = False
|
|
|
128 if verbosity >= 4:
|
|
|
129 log.setLevel(logging.DEBUG)
|
|
|
130 elif verbosity == 3:
|
|
|
131 log.setLevel(logging.INFO)
|
|
|
132 elif verbosity == 2:
|
|
|
133 log.setLevel(logging.WARNING)
|
|
|
134 elif verbosity == 1:
|
|
|
135 log.setLevel(logging.ERROR)
|
|
|
136 elif verbosity == 0:
|
|
|
137 log.disabled = True
|
|
|
138
|
|
|
139 setLevel = staticmethod(setLevel)
|
