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1 from copy import deepcopy
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2 from commons.core.sql.TableSetAdaptator import TableSetAdaptator
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3 from commons.core.coord.Map import Map
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4 from commons.core.coord.Set import Set
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5 import os
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6
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7 class ConvSetChr2Chunk(object):
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8
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9 def __init__(self, db, table, chunk_table, outtable):
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10 self._tablename = table
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11 self._chunk_table = chunk_table
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12 self._db = db
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13 self._outtable = outtable
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14
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15 def convert(self):
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16 """
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17 Convert a 'set' table format.
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18 """
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19 temp_file = str(os.getpid()) + ".on_chunk"
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20 fout = open(temp_file,'w')
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21
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22 str_mask = "SELECT * FROM "+\
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23 self._chunk_table + " WHERE chr='%s' AND ("+\
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24 "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
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25 " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
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26 " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
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27
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28 iTSA = TableSetAdaptator(self._db, self._tablename)
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29 path_num_list = iTSA.getIdList()
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30
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31 for path_num in path_num_list:
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32 slist = iTSA.getSetListFromId(path_num)
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33 for r in slist:
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34 sql_cmd = str_mask%(r.seqname,r.getMin(),r.getMax(),r.getMin(),r.getMax())
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35 self._db.execute(sql_cmd)
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36 res = self._db.fetchall()
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37 for i in res:
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38 chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
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39
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40 new_r = Set()
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41 new_r = deepcopy(r)
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42 new_r.seqname = chunk.name
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43
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44 if (r.start > chunk.start and r.start < chunk.end):
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45 new_r.start = r.start - chunk.start + 1
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46 if (r.end > chunk.start and r.end < chunk.end):
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47 new_r.end = r.end - chunk.start + 1
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48
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49 if r.isOnDirectStrand():
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50 if r.start <= chunk.start:
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51 new_r.start = 1
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52 if r.end >= chunk.end:
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53 new_r.end = chunk.end - chunk.start + 1
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54 else:
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55 if r.end <= chunk.start:
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56 new_r.end = 1
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57 if r.start >= chunk.end:
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58 new_r.start = chunk.end - chunk.start + 1
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59
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60 new_r.write(fout)
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61
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62 fout.close()
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63
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64 self._db.createTable(self._outtable, "set", temp_file)
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65
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66 os.remove(temp_file) |
