Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/structure/Mapping.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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1 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 #
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30 from SMART.Java.Python.structure.SubMapping import SubMapping
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31 from SMART.Java.Python.structure.Transcript import Transcript
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32 from SMART.Java.Python.structure.Interval import Interval
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33
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34 class Mapping(object):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 """A class that represents a mapping"""
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36
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37 def __init__(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 self.targetInterval = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 self.queryInterval = None
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40 self.subMappings = []
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41 self.size = None
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42 self.transcript = None
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43 self.tags = {}
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44
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45
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46 def copy(self, mapping):
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47 for subMapping in mapping.subMappings:
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48 newSubMapping = SubMapping(subMapping)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 self.addSubMapping(newSubMapping)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 self.targetInterval = Interval(mapping.targetInterval)
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51 self.queryInterval = Interval(mapping.queryInterval)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 self.size = mapping.size
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53 self.tags = {}
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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54 for tag in mapping.tags:
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55 self.tags[tag] = mapping[tag]
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56 self.transcript.copy(mapping.transcript)
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57
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58
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59 def setTargetInterval(self, interval):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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60 self.targetInterval = Interval(interval)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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61 if self.queryInterval != None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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62 self.setDirection(self.targetInterval.getDirection() * self.queryInterval.getDirection())
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63
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64
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65 def setQueryInterval(self, interval):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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66 self.queryInterval = Interval(interval)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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67 if self.targetInterval != None:
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68 self.setDirection(self.targetInterval.getDirection() * self.queryInterval.getDirection())
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69
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70
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71 def getQueryInterval(self):
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72 return self.queryInterval
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73
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74
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75 def addSubMapping(self, subMapping):
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76 subMappingCopy = SubMapping(subMapping)
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77 self.subMappings.append(subMappingCopy)
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78
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79 if self.targetInterval:
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80 self.targetInterval.setStart(min(self.targetInterval.getStart(), subMapping.targetInterval.getStart()))
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81 self.targetInterval.setEnd(max(self.targetInterval.getEnd(), subMapping.targetInterval.getEnd()))
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82 else:
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83 self.setTargetInterval(subMapping.targetInterval)
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84 if self.queryInterval:
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85 self.queryInterval.setStart(min(self.queryInterval.getStart(), subMapping.queryInterval.getStart()))
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86 self.queryInterval.setEnd(max(self.queryInterval.getEnd(), subMapping.queryInterval.getEnd()))
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87 else:
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88 self.setQueryInterval(subMapping.queryInterval)
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89
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90 if self.getDirection() != 0:
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91 subMapping.setDirection(self.getDirection())
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92 if self.size == None:
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93 self.size = 0
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94 if "identity" in subMapping.getTagNames() and "identity" not in self.getTagNames():
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95 self.setTagValue("identity", subMapping.getTagValue("identity"))
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96 elif "identity" in subMapping.getTagNames() and subMapping.size != None:
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97 self.setTagValue("identity", (self.getTagValue("identity") * self.size + subMapping.getTagValue("identity") * subMapping.size) / (self.size + subMapping.size))
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98 if subMapping.size != None:
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99 self.size += subMapping.size
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100 if "nbMismatches" in subMapping.getTagNames() and "nbMismatches" not in self.getTagNames():
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101 self.setTagValue("nbMismatches", subMapping.getTagValue("nbMismatches"))
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102 elif "nbMismatches" in subMapping.getTagNames():
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103 self.setTagValue("nbMismatches", self.getTagValue("nbMismatches") + subMapping.getTagValue("nbMismatches"))
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104 if "nbGaps" in subMapping.getTagNames() and "nbGaps" not in self.getTagNames():
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105 self.setTagValue("nbGaps", subMapping.getTagValue("nbGaps"))
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106 elif "nbGaps" in subMapping.getTagNames():
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107 self.setTagValue("nbGaps", self.getTagValue("nbGaps") + subMapping.getTagValue("nbGaps"))
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108
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109
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110 def setDirection(self, direction):
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111 for subMapping in self.subMappings:
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112 subMapping.setDirection(direction)
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113
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114
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115 def getDirection(self):
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116 if not self.subMappings:
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117 raise Exception("Error! Mapping '%s' has no submapping" % (self))
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118 return self.subMappings[0].getDirection()
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119
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120
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121 def setSize(self, size):
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122 self.size = size
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123 if "identity" in self.getTagNames():
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124 self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
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125
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126
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127 def setTagValue(self, name, value):
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128 self.tags[name] = value
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129 self.transcript = None
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130
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
131
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yufei-luo
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132 def getTagValue(self, name):
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133 return self.tags[name]
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134
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135
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yufei-luo
parents:
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136 def getTagNames(self):
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yufei-luo
parents:
diff changeset
137 return self.tags.keys()
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138
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139
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yufei-luo
parents:
diff changeset
140 def setIdentity(self, identity):
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yufei-luo
parents:
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141 self.setTagValue("identity", identity)
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yufei-luo
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diff changeset
142 if self.size != None and "nbMismatches" not in self.getTagNames():
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143 nbMismatches = 0 if self.size == 0 else self.size - round(self.size * self.getTagValue("identity") / 100.0)
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yufei-luo
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144 self.setTagValue("nbMismatches", nbMismatches)
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145
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146
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147 def setNbOccurrences(self, nbOccurrences):
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148 self.setTagValue("nbOccurrences", nbOccurrences)
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149
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150
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151 def setNbMismatches(self, nbMismatches):
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parents:
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152 self.setTagValue("nbMismatches", nbMismatches)
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yufei-luo
parents:
diff changeset
153 if self.size != None and "identity" not in self.getTagNames():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
diff changeset
154 identity = 100 if self.size == 0 else (self.size - self.getTagValue("nbMismatches")) / float(self.size) * 100
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yufei-luo
parents:
diff changeset
155 self.setTagValue("identity", identity)
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diff changeset
156
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157
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yufei-luo
parents:
diff changeset
158 def setNbGaps(self, nbGaps):
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yufei-luo
parents:
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159 self.setTagValue("nbGaps", nbGaps)
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160
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161
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yufei-luo
parents:
diff changeset
162 def setRank(self, rank):
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yufei-luo
parents:
diff changeset
163 self.setTagValue("rank", rank)
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diff changeset
164
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165
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yufei-luo
parents:
diff changeset
166 def setEvalue(self, evalue):
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yufei-luo
parents:
diff changeset
167 self.setTagValue("evalue", evalue)
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diff changeset
168
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169
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yufei-luo
parents:
diff changeset
170 def setOccurrence(self, occurrence):
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yufei-luo
parents:
diff changeset
171 self.setTagValue("occurrence", occurrence)
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diff changeset
172
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173
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yufei-luo
parents:
diff changeset
174 def setBestRegion(self, bestRegion):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
175 self.setTagValue("bestRegion", bestRegion)
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diff changeset
176
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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177
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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178 def mergeExons(self, distance):
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179 previousSubMapping = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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180 subMappings = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
181 for subMapping in self.subMappings:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
182 if previousSubMapping == None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
183 subMappings.append(subMapping)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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184 previousSubMapping = subMapping
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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185 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
186 targetDistance = subMapping.targetInterval.getDistance(previousSubMapping.targetInterval)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
187 queryDistance = subMapping.queryInterval.getDistance(previousSubMapping.queryInterval)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
188 if targetDistance <= distance:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
189 self.setTagValue("nbGaps", self.getTagValue("nbGaps") + queryDistance)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
190 previousSubMapping.merge(subMapping)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
191 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
192 subMappings.append(subMapping)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
193 previousSubMapping = subMapping
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yufei-luo
parents:
diff changeset
194 self.subMappings = subMappings
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195
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196
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yufei-luo
parents:
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197 def getTranscript(self):
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198 """
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199 Extract a transcript from this mapping
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200 @return: a transcript
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yufei-luo
parents:
diff changeset
201 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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202 if self.transcript != None:
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yufei-luo
parents:
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203 return self.transcript
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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204 self.transcript = Transcript()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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205 self.transcript.copy(self.targetInterval)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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206 self.transcript.setDirection(self.getDirection())
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
207 self.transcript.setName(self.queryInterval.getName())
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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208 self.transcript.removeExons()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
209 if len(self.subMappings) > 1:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
210 for subMapping in self.subMappings:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
211 self.transcript.addExon(subMapping.targetInterval)
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yufei-luo
parents:
diff changeset
212 cpt = 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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213 for exon in self.transcript.exons:
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yufei-luo
parents:
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214 exon.setDirection(self.transcript.getDirection())
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
215 exon.setName("%s-exon%d" % (self.transcript.getName(), cpt))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
216 exon.setChromosome(self.transcript.getChromosome())
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
217 cpt += 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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218 self.transcript.setDirection(self.getDirection())
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
219 self.transcript.sortExons()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
220 for tag in self.tags:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
221 if "bestRegion" not in self.getTagNames():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
222 self.transcript.setTagValue("bestRegion", "(self)")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
223 self.transcript.setTagValue(tag, self.getTagValue(tag))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
224 return self.transcript
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
225
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
226
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
227 def getChromosome(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
228 if not self.subMappings:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
229 raise Exception("Error! Mapping '%s' has no submapping" % (self))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
230 return self.subMappings[0].targetInterval.getChromosome()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
231
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
232
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
233
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
234 def getErrorScore(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
235 return self.getTagValue("nbGaps") * 3 + self.getTagValue("nbMismatches") + (len(self.subMappings) - 1) * 0.1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
236
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
237
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
238 def printGBrowseReference(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
239 return self.getTranscript().printGBrowseReference()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
240
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
241
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
242 def printGBrowseLine(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
243 return self.getTranscript().printGBrowseLine()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
244
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
245
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
246 def printGBrowse(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
247 return self.getTranscript().printGBrowse()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
248
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
249
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
250 def printBed(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
251 return self.getTranscript().printBed()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
252
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
253
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
254 def __str__(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
255 return "%s ---- %s" % (str(self.getTranscript()), ", ". join([str(submapping) for submapping in self.subMappings]))