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1 from copy import deepcopy
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2 from commons.core.sql.TablePathAdaptator import TablePathAdaptator
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3 from commons.core.coord.PathUtils import PathUtils
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4 from commons.core.coord.Map import Map
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5 from commons.core.coord.Path import Path
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6 import os
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7
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8 class ConvPathChr2Chunk(object):
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9
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10 def __init__(self, db, table, chunk_table, outtable):
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11 self._tablename = table
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12 self._chunk_table = chunk_table
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13 self._db = db
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14 self._outtable = outtable
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15
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16 def convert(self):
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17 """
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18 Convert a 'path' table format.
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19 """
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20 temp_file = str(os.getpid()) + ".on_chunk"
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21 fout = open(temp_file,'w')
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22
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23 str_mask = "SELECT * FROM "+\
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24 self._chunk_table + " WHERE chr='%s' AND ("+\
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25 "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
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26 " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
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27 " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
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28
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29 iTPA = TablePathAdaptator(self._db, self._tablename)
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30 path_num_list = iTPA.getIdList()
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31
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32 for path_num in path_num_list:
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33 slist = iTPA.getPathListFromId(path_num)
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34 for r in slist:
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35 r_min, r_max = PathUtils.getQueryMinMaxFromPathList([r])
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36 sql_cmd = str_mask%(r.range_query.seqname,r_min,r_max,r_min,r_max)
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37 self._db.execute(sql_cmd)
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38 res = self._db.fetchall()
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39 for i in res:
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40 chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
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41
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42 new_r = Path()
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43 new_r = deepcopy(r)
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44 new_r.range_query.seqname = chunk.name
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45
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46 if (r.range_query.start > chunk.start and r.range_query.start < chunk.end):
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47 new_r.range_query.start = r.range_query.start - chunk.start + 1
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48 if (r.range_query.end > chunk.start and r.range_query.end < chunk.end):
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49 new_r.range_query.end = r.range_query.end - chunk.start + 1
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50
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51 if r.range_query.isOnDirectStrand():
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52 if r.range_query.start <= chunk.start:
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53 new_r.range_query.start = 1
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54 if r.range_query.end >= chunk.end:
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55 new_r.range_query.end = chunk.end - chunk.start + 1
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56 else:
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57 if r.range_query.end <= chunk.start:
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58 new_r.range_query.end = 1
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59 if r.range_query.start >= chunk.end:
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60 new_r.range_query.start = chunk.end - chunk.start + 1
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61
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62 new_r.write(fout)
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63
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64 fout.close()
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65
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66 self._db.createTable(self._outtable, "path", temp_file)
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67
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68 os.remove(temp_file) |
