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32
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1 from galaxy.datatypes.data import Text
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31
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2 from galaxy.datatypes.tabular import Tabular
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35
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3 from galaxy.datatypes.binary import SQlite
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4
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4
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35
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5 class FlapjackFormat(SQlite):
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9
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6 file_ext = "flapjack"
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35
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7
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8 def sniff(self, filename):
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9 if super(FlapjackFormat, self).sniff(filename):
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10 fj_table_names = ["objects", "project"]
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11 try:
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36
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12 conn = sqlite.connect(filename)
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35
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13 c = conn.cursor()
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14 tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
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15 result = c.execute(tables_query).fetchall()
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16 result = [_[0] for _ in result]
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17 for table_name in fj_table_names:
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18 if table_name not in result:
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19 return False
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20 return True
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21 except Exception as e:
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36
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22 log.warning('%s, sniff Exception: %s', self, e)
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35
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23 return False
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38
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24
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25 Binary.register_sniffable_binary_format( "flapjack", "flapjack", FlapjackFormat)
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9
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26
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28
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27 class FlapjackMapFormat(Tabular):
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4
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28 file_ext = "fjmap"
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29
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30 def sniff( self, filename ):
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31 h = open(filename)
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32 line = h.readline()
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33 if line.rstrip() != "# fjFile = MAP":
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34 h.close()
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35 return False
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36 return True
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37
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28
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38 class FlapjackGenotypeFormat(Tabular):
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4
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39 file_ext = "fjgenotype"
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40
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41 def sniff( self, filename ):
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42 h = open(filename)
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43 line = h.readline()
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44 if line.rstrip() != "# fjFile = GENOTYPE":
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45 h.close()
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46 return False
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47 return True
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48
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28
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49 class FlapjackPhenotypeFormat(Tabular):
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4
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50 file_ext = "fjphenotye"
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51
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52 def sniff( self, filename ):
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53 h = open(filename)
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54 line = h.readline()
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55 if line.rstrip() != "# fjFile = PHENOTYPE":
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56 h.close()
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57 return False
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58 return True
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59
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28
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60 class FlapjackQtlFormat(Tabular):
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4
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61 file_ext = "fjqtl"
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62
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63 def sniff( self, filename ):
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64 h = open(filename)
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65 line = h.readline()
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66 if line.rstrip() != "# fjFile = QTL":
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67 h.close()
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68 return False
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69 return True
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70
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28
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71 class FlapjackGraphFormat(Tabular):
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4
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72 file_ext = "fjgraph"
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73
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74 def sniff( self, filename ):
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75 h = open(filename)
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76 line = h.readline()
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77 if line.rstrip() != "# fjFile = GRAPH":
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78 h.close()
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79 return False
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80 return True |
