Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervalsBin.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python |
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2 # |
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3 # Copyright INRA-URGI 2009-2011 |
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4 # |
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5 # This software is governed by the CeCILL license under French law and |
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6 # abiding by the rules of distribution of free software. You can use, |
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7 # modify and/ or redistribute the software under the terms of the CeCILL |
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8 # license as circulated by CEA, CNRS and INRIA at the following URL |
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9 # "http://www.cecill.info". |
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10 # |
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11 # As a counterpart to the access to the source code and rights to copy, |
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12 # modify and redistribute granted by the license, users are provided only |
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13 # with a limited warranty and the software's author, the holder of the |
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14 # economic rights, and the successive licensors have only limited |
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15 # liability. |
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16 # |
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17 # In this respect, the user's attention is drawn to the risks associated |
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18 # with loading, using, modifying and/or developing or reproducing the |
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19 # software by the user in light of its specific status of free software, |
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20 # that may mean that it is complicated to manipulate, and that also |
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21 # therefore means that it is reserved for developers and experienced |
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22 # professionals having in-depth computer knowledge. Users are therefore |
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23 # encouraged to load and test the software's suitability as regards their |
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24 # requirements in conditions enabling the security of their systems and/or |
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25 # data to be ensured and, more generally, to use and operate it in the |
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26 # same conditions as regards security. |
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27 # |
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28 # The fact that you are presently reading this means that you have had |
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29 # knowledge of the CeCILL license and that you accept its terms. |
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30 # |
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31 import random, os, os.path, time, sqlite3 |
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32 from optparse import OptionParser |
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33 from commons.core.parsing.ParserChooser import ParserChooser |
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34 from commons.core.writer.TranscriptWriter import TranscriptWriter |
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35 from SMART.Java.Python.structure.Interval import Interval |
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36 from SMART.Java.Python.structure.Transcript import Transcript |
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37 from SMART.Java.Python.structure.Mapping import Mapping |
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38 from SMART.Java.Python.misc.Progress import Progress |
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39 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress |
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40 try: |
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41 import cPickle as pickle |
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42 except: |
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43 import pickle |
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44 |
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45 MINBIN = 3 |
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46 MAXBIN = 7 |
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47 |
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48 |
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49 def getBin(start, end): |
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50 for i in range(MINBIN, MAXBIN + 1): |
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51 binLevel = 10 ** i |
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52 if int(start / binLevel) == int(end / binLevel): |
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53 return int(i * 10 ** (MAXBIN + 1) + int(start / binLevel)) |
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54 return int((MAXBIN + 1) * 10 ** (MAXBIN + 1)) |
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55 |
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56 def getOverlappingBins(start, end): |
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57 array = [] |
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58 bigBin = int((MAXBIN + 1) * 10 ** (MAXBIN + 1)) |
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59 for i in range(MINBIN, MAXBIN + 1): |
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60 binLevel = 10 ** i |
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61 array.append((int(i * 10 ** (MAXBIN + 1) + int(start / binLevel)), int(i * 10 ** (MAXBIN + 1) + int(end / binLevel)))) |
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62 array.append((bigBin, bigBin)) |
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63 return array |
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64 |
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65 |
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66 class FindOverlapsWithSeveralIntervalsBin(object): |
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67 |
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68 def __init__(self, verbosity): |
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69 self.verbosity = verbosity |
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70 self.randomNumber = random.randint(0, 10000) |
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71 self.dbName = "smartdb%d" % (self.randomNumber) |
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72 if "SMARTTMPPATH" in os.environ: |
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73 self.dbName = os.join(os.environ["SMARTTMPPATH"], self.dbName) |
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74 self.connection = sqlite3.connect(self.dbName) |
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75 self.tableNames = {} |
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76 self.nbQueries = 0 |
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77 self.nbRefs = 0 |
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78 self.nbWritten = 0 |
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79 self.nbOverlaps = 0 |
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80 cursor = self.connection.cursor() |
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81 cursor.execute("PRAGMA journal_mode = OFF") |
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82 cursor.execute("PRAGMA synchronous = 0") |
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83 cursor.execute("PRAGMA locking_mode = EXCLUSIVE") |
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84 cursor.execute("PRAGMA count_change = OFF") |
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85 cursor.execute("PRAGMA temp_store = 2") |
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86 |
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87 def __del__(self): |
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88 cursor = self.connection.cursor() |
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89 for tableName in self.tableNames.values(): |
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90 cursor.execute("DROP TABLE IF EXISTS %s" % (tableName)) |
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91 if os.path.exists(self.dbName): |
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92 os.remove(self.dbName) |
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93 |
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94 def createTable(self, chromosome): |
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95 cursor = self.connection.cursor() |
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96 tableName = "tmpTable_%s_%d" % (chromosome.replace("-", "_"), self.randomNumber) |
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97 cursor.execute("CREATE TABLE %s (start INT, end INT, transcript BLOB, bin INT)" % (tableName)) |
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98 cursor.execute("CREATE INDEX index_%s ON %s (bin)" % (tableName, tableName)) |
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99 self.tableNames[chromosome] = tableName |
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100 |
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101 def setReferenceFile(self, fileName, format): |
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102 chooser = ParserChooser(self.verbosity) |
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103 chooser.findFormat(format) |
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104 parser = chooser.getParser(fileName) |
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105 startTime = time.time() |
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106 if self.verbosity > 2: |
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107 print "Storing into table" |
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108 for transcript in parser.getIterator(): |
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109 if transcript.__class__.__name__ == "Mapping": |
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110 transcript = transcript.getTranscript() |
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111 transcriptString = pickle.dumps(transcript) |
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112 chromosome = transcript.getChromosome() |
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113 if chromosome not in self.tableNames: |
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114 self.createTable(chromosome) |
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115 start = transcript.getStart() |
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116 end = transcript.getEnd() |
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117 bin = getBin(start, end) |
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118 cursor = self.connection.cursor() |
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119 cursor.execute("INSERT INTO %s (start, end, transcript, bin) VALUES (?, ?, ?, ?)" % (self.tableNames[chromosome]), (start, end, sqlite3.Binary(transcriptString), bin)) |
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120 self.nbRefs += 1 |
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121 self.connection.commit() |
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122 endTime = time.time() |
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123 if self.verbosity > 2: |
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124 print " ...done (%.2gs)" % (endTime - startTime) |
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125 |
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126 def setQueryFile(self, fileName, format): |
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127 chooser = ParserChooser(self.verbosity) |
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128 chooser.findFormat(format) |
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129 self.queryParser = chooser.getParser(fileName) |
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130 self.nbQueries = self.queryParser.getNbItems() |
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131 |
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132 def setOutputFile(self, fileName): |
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133 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity) |
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134 |
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135 def compare(self): |
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136 progress = Progress(self.nbQueries, "Reading queries", self.verbosity) |
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137 startTime = time.time() |
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138 for queryTranscript in self.queryParser.getIterator(): |
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139 if queryTranscript.__class__.__name__ == "Mapping": |
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140 queryTranscript = queryTranscript.getTranscript() |
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141 progress.inc() |
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142 queryChromosome = queryTranscript.getChromosome() |
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143 if queryChromosome not in self.tableNames: |
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144 continue |
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145 queryStart = queryTranscript.getStart() |
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146 queryEnd = queryTranscript.getEnd() |
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147 bins = getOverlappingBins(queryStart, queryEnd) |
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148 commands = [] |
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149 for bin in bins: |
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150 command = "SELECT * FROM %s WHERE bin " % (self.tableNames[queryChromosome]) |
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151 if bin[0] == bin[1]: |
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152 command += "= %d" % (bin[0]) |
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153 else: |
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154 command += "BETWEEN %d AND %d" % (bin[0], bin[1]) |
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155 commands.append(command) |
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156 command = " UNION ".join(commands) |
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157 cursor = self.connection.cursor() |
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158 cursor.execute(command) |
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159 overlap = False |
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160 line = cursor.fetchone() |
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161 while line: |
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162 refStart, refEnd, refTranscriptString, refBin = line |
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163 if refStart <= queryEnd and refEnd >= queryStart: |
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164 refTranscript = pickle.loads(str(refTranscriptString)) |
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165 if refTranscript.overlapWith(queryTranscript): |
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166 overlap = True |
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167 self.nbOverlaps += 1 |
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168 line = cursor.fetchone() |
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169 if overlap: |
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170 self.writer.addTranscript(queryTranscript) |
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171 self.nbWritten += 1 |
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172 progress.done() |
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173 endTime = time.time() |
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174 self.timeSpent = endTime - startTime |
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175 |
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176 def displayResults(self): |
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177 print "# queries: %d" % (self.nbQueries) |
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178 print "# refs: %d" % (self.nbRefs) |
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179 print "# written: %d (%d overlaps)" % (self.nbWritten, self.nbOverlaps) |
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180 print "time: %.2gs" % (self.timeSpent) |
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181 |
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182 def run(self): |
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183 self.compare() |
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184 self.displayResults() |
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185 |
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186 if __name__ == "__main__": |
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187 |
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188 description = "Find Overlaps With Several Intervals Using Bin v1.0.1: Use MySQL binning to compare intervals. [Category: Personal]" |
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189 |
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190 parser = OptionParser(description = description) |
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191 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="query input file [compulsory] [format: file in transcript format given by -f]") |
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192 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]") |
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193 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]") |
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194 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]") |
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195 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]") |
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196 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") |
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197 (options, args) = parser.parse_args() |
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198 |
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199 fowsib = FindOverlapsWithSeveralIntervalsBin(options.verbosity) |
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200 fowsib.setQueryFile(options.inputFileName1, options.format1) |
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201 fowsib.setReferenceFile(options.inputFileName2, options.format2) |
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202 fowsib.setOutputFile(options.outputFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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203 fowsib.run() |
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204 |