Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/SequenceListParser.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
---|---|
date | Fri, 18 Jan 2013 04:54:14 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
5:ea3082881bf8 | 6:769e306b7933 |
---|---|
1 # | |
2 # Copyright INRA-URGI 2009-2010 | |
3 # | |
4 # This software is governed by the CeCILL license under French law and | |
5 # abiding by the rules of distribution of free software. You can use, | |
6 # modify and/ or redistribute the software under the terms of the CeCILL | |
7 # license as circulated by CEA, CNRS and INRIA at the following URL | |
8 # "http://www.cecill.info". | |
9 # | |
10 # As a counterpart to the access to the source code and rights to copy, | |
11 # modify and redistribute granted by the license, users are provided only | |
12 # with a limited warranty and the software's author, the holder of the | |
13 # economic rights, and the successive licensors have only limited | |
14 # liability. | |
15 # | |
16 # In this respect, the user's attention is drawn to the risks associated | |
17 # with loading, using, modifying and/or developing or reproducing the | |
18 # software by the user in light of its specific status of free software, | |
19 # that may mean that it is complicated to manipulate, and that also | |
20 # therefore means that it is reserved for developers and experienced | |
21 # professionals having in-depth computer knowledge. Users are therefore | |
22 # encouraged to load and test the software's suitability as regards their | |
23 # requirements in conditions enabling the security of their systems and/or | |
24 # data to be ensured and, more generally, to use and operate it in the | |
25 # same conditions as regards security. | |
26 # | |
27 # The fact that you are presently reading this means that you have had | |
28 # knowledge of the CeCILL license and that you accept its terms. | |
29 # | |
30 import sys | |
31 from SMART.Java.Python.structure.SequenceList import SequenceList | |
32 from SMART.Java.Python.misc.Progress import Progress | |
33 | |
34 class SequenceListParser(object): | |
35 """ | |
36 A virtual class that reads a list of sequences | |
37 @ivar verbosity: verbosity | |
38 @type verbosity: int | |
39 @ivar fileName: name of the file to parse | |
40 @type fileName: string | |
41 @ivar handle: file to parse | |
42 @type handle: file | |
43 @ivar nbSequences: number of sequences in the file | |
44 @type nbSequences: int | |
45 @ivar nbReadSequences: number of sequences read | |
46 @type nbReadSequences: int | |
47 @ivar currentLine: line currently read | |
48 @type currentLine: string | |
49 @ivar size: total number of nucleotides in the sequences | |
50 @type size: int | |
51 @ivar sizes: number of nucleotides per sequences | |
52 @type sizes: dict of string to int | |
53 """ | |
54 | |
55 def __init__(self, fileName, verbosity = 0): | |
56 """ | |
57 Constructor | |
58 @param verbosity: verbosity | |
59 @type verbosity: int | |
60 @param fileName: name of the file to parse | |
61 @type fileName: string | |
62 """ | |
63 self.verbosity = verbosity | |
64 self.fileName = fileName | |
65 self.nbSequences = None | |
66 self.nbReadSequences = 0 | |
67 self.currentLine = None | |
68 self.size = None | |
69 self.sizes = None | |
70 try: | |
71 self.handle = open(self.fileName, "rb") | |
72 except IOError: | |
73 raise Exception("Error! Sequence file '%s' does not exist! Exiting..." % (self.fileName)) | |
74 | |
75 | |
76 def __del__(self): | |
77 """ | |
78 Destructor | |
79 """ | |
80 if not self.handle.closed: | |
81 self.handle.close() | |
82 | |
83 | |
84 def close(self): | |
85 """ | |
86 Close file handle | |
87 """ | |
88 self.handle.close() | |
89 | |
90 | |
91 def reset(self): | |
92 """ | |
93 Prepare the file to be read again from start | |
94 """ | |
95 self.handle.seek(0) | |
96 self.currentLine = None | |
97 self.nbReadSequences = 0 | |
98 | |
99 | |
100 def getFileFormats(self): | |
101 pass | |
102 getFileFormats = staticmethod(getFileFormats) | |
103 | |
104 | |
105 def parse(self): | |
106 """ | |
107 Parse the whole file in one shot | |
108 @return: a list of sequence | |
109 """ | |
110 sequenceList = SequenceList() | |
111 progress = Progress(self.getNbSequences(), "Reading %s" % (self.fileName), self.verbosity) | |
112 for sequence in self.getIterator(): | |
113 sequenceList.addSequence(sequence) | |
114 progress.inc() | |
115 progress.done() | |
116 return sequenceList | |
117 | |
118 | |
119 def getIterator(self): | |
120 """ | |
121 Iterate on the file, sequence by sequence | |
122 @return: an iterator to sequences | |
123 """ | |
124 self.reset() | |
125 sequence = self.parseOne() | |
126 while sequence != None: | |
127 self.nbReadSequences += 1 | |
128 yield sequence | |
129 sequence = self.parseOne() | |
130 | |
131 | |
132 def getInfos(self): | |
133 """ | |
134 Get some generic information about the sequences | |
135 """ | |
136 self.nbSequences = 0 | |
137 self.size = 0 | |
138 self.reset() | |
139 if self.verbosity >= 10: | |
140 print "Getting information on %s." % (self.fileName) | |
141 for sequence in self.getIterator(): | |
142 self.nbSequences += 1 | |
143 self.size += sequence.getSize() | |
144 if self.verbosity >= 10 and self.nbSequences % 100000 == 0: | |
145 sys.stdout.write(" %d sequences read\r" % (self.nbSequences)) | |
146 sys.stdout.flush() | |
147 self.reset() | |
148 if self.verbosity >= 10: | |
149 print " %d sequences read" % (self.nbSequences) | |
150 print "Done." | |
151 | |
152 | |
153 def getNbSequences(self): | |
154 """ | |
155 Get the number of sequences in the file | |
156 @return: the number of sequences | |
157 """ | |
158 if self.nbSequences != None: | |
159 return self.nbSequences | |
160 self.getInfos() | |
161 return self.nbSequences | |
162 | |
163 | |
164 def getNbItems(self): | |
165 """ | |
166 Get the number of sequences in the file | |
167 @return: the number of sequences | |
168 """ | |
169 return self.getNbSequences() | |
170 | |
171 | |
172 def getSize(self): | |
173 """ | |
174 Get the size of all the sequences | |
175 @return: the size | |
176 """ | |
177 if self.size != None: | |
178 return self.size | |
179 self.getInfos() | |
180 return self.size | |
181 | |
182 | |
183 def getRegions(self): | |
184 """ | |
185 Get the names of the sequences | |
186 @return: the names | |
187 """ | |
188 if self.sizes != None: | |
189 return self.sizes.keys() | |
190 | |
191 self.sizes = {} | |
192 self.reset() | |
193 if self.verbosity >= 10: | |
194 print "Getting information on %s." % (self.fileName) | |
195 self.nbSequences = 0 | |
196 for sequence in self.getIterator(): | |
197 self.sizes[sequence.name] = sequence.getSize() | |
198 self.nbSequences += 1 | |
199 if self.verbosity >= 10 and self.nbSequences % 100000 == 0: | |
200 sys.stdout.write(" %d sequences read\r" % (self.nbSequences)) | |
201 sys.stdout.flush() | |
202 self.reset() | |
203 if self.verbosity >= 10: | |
204 print " %d sequences read" % (self.nbSequences) | |
205 print "Done." | |
206 return self.sizes.keys() | |
207 | |
208 | |
209 def getSizeOfRegion(self, region): | |
210 """ | |
211 Get the size of a sequence | |
212 @param region: the name of the sequence | |
213 @type region: string | |
214 @return: the size of the sequence | |
215 """ | |
216 if self.sizes != None: | |
217 if region not in self.sizes: | |
218 raise Exception("Region %s is not found" % region) | |
219 return self.sizes[region] | |
220 | |
221 self.getRegions() | |
222 if region not in self.sizes: | |
223 raise Exception("Region %s is not found" % region) | |
224 | |
225 def __eq__(self, o): | |
226 if o == None: | |
227 return False | |
228 return self.fileName == o.fileName and self.nbSequences == o.nbSequences |