Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/structure/TranscriptList.py @ 38:2c0c0a89fad7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
parents 769e306b7933
children
comparison
equal deleted inserted replaced
37:d22fadc825e3 38:2c0c0a89fad7
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 from SMART.Java.Python.structure.Transcript import Transcript
31 from SMART.Java.Python.mySql.MySqlTable import MySqlTable
32 from SMART.Java.Python.structure.Interval import Interval
33 from SMART.Java.Python.misc.Progress import Progress
34
35
36 class TranscriptList(object):
37 """A class that codes for a list of transcript"""
38
39 def __init__(self, verbosity = 0):
40 self.transcripts = dict()
41 self.longestTranscript = 0
42 self.verbosity = verbosity
43
44
45 def getTranscript(self, chromosome, index):
46 return self.transcripts[chromosome][index]
47
48
49 def getChromosomes(self):
50 return self.transcripts.keys()
51
52
53 def getTranscriptsOnChromosome(self, chromosome):
54 if chromosome not in self.transcripts:
55 return []
56 return self.transcripts[chromosome]
57
58
59 def addTranscript(self, transcript):
60 if transcript.getChromosome() in self.transcripts:
61 self.transcripts[transcript.getChromosome()].append(transcript)
62 else:
63 self.transcripts[transcript.getChromosome()] = [transcript]
64 self.longestTranscript = max(self.longestTranscript, transcript.getEnd() - transcript.getStart())
65
66
67 def removeTranscript(self, chromosome, i):
68 del self.transcripts[chromosome][i]
69
70
71 def removeAll(self):
72 self.transcripts = {}
73
74
75 def getNbTranscripts(self):
76 nbTranscripts = 0
77 for chromosome in self.transcripts:
78 nbTranscripts += len(self.transcripts[chromosome])
79 return nbTranscripts
80
81
82 def getSize(self):
83 size = 0
84 for chromosome in self.transcripts:
85 for transcript in self.transcripts[chromosome]:
86 size += transcript.getSize()
87 return size
88
89
90 def sort(self):
91 for chromosome in self.transcripts:
92 self.transcripts[chromosome].sort(lambda x, y: x.getStart() - y.getStart())
93
94
95 def removeOverlapWith(self, transcriptList):
96 transcriptList.sort()
97 for chromosome in self.transcripts:
98 progress = Progress(len(self.transcripts[chromosome]), "Handling chromosome %s" % (chromosome), self.verbosity)
99 for thisTranscriptId in range(len(self.transcripts[chromosome])):
100 progress.inc()
101 for thatTranscriptId in range(len(transcriptList.transcripts[chromosome])):
102 if self.transcripts[chromosome][thisTranscriptId].overlapWith(transcriptList.transcripts[chromosome][thatTranscriptId]):
103 self.transcripts[chromosome][thisTranscriptId] = None
104 break
105 if self.transcripts[chromosome][thisTranscriptId].getEnd() > transcriptList.transcripts[chromosome][thatTranscriptId]:
106 break
107 self.transcripts[chromosome] = [transcript for transcript in self.transcripts[chromosome] if transcript != None]
108 progress.done()
109
110
111 def removeOverlapWithExon(self, transcriptList):
112 transcriptList.sort()
113 for chromosome in self.transcripts:
114 progress = Progress(len(self.transcripts[chromosome]), "Handling chromosome %s" % (chromosome), self.verbosity)
115 for thisTranscriptId in range(len(self.transcripts[chromosome])):
116 progress.inc()
117 for thatTranscriptId in range(len(transcriptList.transcripts[chromosome])):
118 if self.transcripts[chromosome][thisTranscriptId].overlapWithExon(transcriptList.transcripts[chromosome][thatTranscriptId]):
119 self.transcripts[chromosome][thisTranscriptId] = None
120 break
121 if self.transcripts[chromosome][thisTranscriptId].getEnd() > transcriptList.transcripts[chromosome][thatTranscriptId]:
122 break
123 self.transcripts[chromosome] = [transcript for transcript in self.transcripts[chromosome] if transcript != None]
124 progress.done()
125
126
127 def setDefaultTagValue(self, name, value):
128 for transcript in self.getIterator():
129 transcript.setTag(name, value)
130
131
132 def storeDatabase(self, mySqlConnection):
133 transcriptsTable = MySqlTable("TmpTranscriptsTable", mySqlConnection)
134 transcriptsTable.create(Transcript.getSqlVariables(), Transcript.getSqlTypes())
135 intervalsVariables = Interval.getSqlVariables()
136 intervalsVariables.append("idTranscript")
137 intervalsTypes = Interval.getSqlTypes()
138 intervalsTypes["idTranscript"] = "int"
139 intervalsTable = MySqlTable("TmpIntervalsTable", mySqlConnection)
140 intervalsTable.create(intervalsVariables, intervalsTypes)
141 for chromosome in self.transcripts:
142 for transcript in self.transcripts[chromosome]:
143 idTranscript = transcriptsTable.addLine(transcript.getSqlValues())
144 for exon in transcript.getExons():
145 intervalValues = exon.getSqlValues()
146 intervalValues["idTranscript"] = idTranscript
147 intervalsTable.addLine(intervalValues)
148
149
150 def getIterator(self):
151 chromosomes = self.transcripts.keys()
152 currentChromosome = 0
153 currentTranscript = 0
154 while True:
155 if currentChromosome >= len(chromosomes):
156 return
157 elif currentTranscript >= len(self.transcripts[chromosomes[currentChromosome]]):
158 currentTranscript = 0
159 currentChromosome += 1
160 elif self.transcripts[chromosomes[currentChromosome]][currentTranscript] == None:
161 currentTranscript += 1
162 else:
163 yield self.transcripts[chromosomes[currentChromosome]][currentTranscript]
164 currentTranscript += 1
165
166
167 def __str__(self):
168 string = ""
169 for transcript in self.getIterator():
170 string += str(transcript)
171 return string
172