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1 from copy import deepcopy
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2 from commons.core.sql.TableMapAdaptator import TableMapAdaptator
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3 from commons.core.coord.Map import Map
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4 import os
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5
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6 class ConvMapChr2Chunk(object):
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7
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8 def __init__(self, db, table, chunk_table, outtable):
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9 self._tablename = table
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10 self._chunk_table = chunk_table
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11 self._db = db
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12 self._outtable = outtable
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13
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14 def convert(self):
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15 """
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16 Convert a 'set' table format.
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17 """
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18 temp_file=str(os.getpid()) + ".on_chunk"
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19 fout=open(temp_file,'w')
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20
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21 str_mask = "SELECT * FROM "+\
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22 self._chunk_table + " WHERE chr='%s' AND ("+\
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23 "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
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24 " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
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25 " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
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26
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27 iTMA = TableMapAdaptator(self._db, self._tablename)
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28 chr_list = iTMA.getSeqNameList()
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29
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30 for chr in chr_list:
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31 mlist = iTMA.getMapListFromChr(chr)
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32 for m in mlist:
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33 sql_cmd = str_mask%(m.seqname,m.getMin(),m.getMax(),m.getMin(),m.getMax())
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34 self._db.execute(sql_cmd)
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35 res = self._db.fetchall()
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36 for i in res:
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37 chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
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38
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39 new_m = deepcopy(m)
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40 new_m.seqname = chunk.name
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41
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42 if (m.start > chunk.start and m.start < chunk.end):
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43 new_m.start = m.start - chunk.start + 1
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44 if (m.end > chunk.start and m.end < chunk.end):
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45 new_m.end = m.end - chunk.start + 1
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46
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47 if m.isOnDirectStrand():
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48 if m.start <= chunk.start:
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49 new_m.start = 1
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50 if m.end >= chunk.end:
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51 new_m.end = chunk.end - chunk.start + 1
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52 else:
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53 if m.end <= chunk.start:
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54 new_m.end = 1
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55 if m.start >= chunk.end:
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56 new_m.start = chunk.end - chunk.start + 1
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57
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58 new_m.write(fout)
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59
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60 fout.close()
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61
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62 self._db.createTable(self._outtable, "map", temp_file)
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63
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64 os.remove(temp_file) |
