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6
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1 import time
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2 import os
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3
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4 class PalsToAlign(object):
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5 """
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6 Convert the output from PALS (GFF2 format) into the 'align' format.
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7 """
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8 def __init__(self,inputPalsFileName="" , outputAlignFileName="", removeSameSequences=False):
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9 self._removeSameSequences = removeSameSequences
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10 self._inputPalsFileName = inputPalsFileName
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11 self._outputAlignFileName = outputAlignFileName
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12
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13 def run (self):
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14 file = open(self._inputPalsFileName, "r")
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15 tmpFileName = "PalsToAlign%s"%str(os.getpid() )
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16 tmpFile = open(tmpFileName, "w")
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17
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18 for line in file.readlines():
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19
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20 if line == "":
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21 break
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22
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23 data = line.split("\t")
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24
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25 qryName = data[0]
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26 source = data[1]
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27 feature = data[2]
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28 qryStart = data[3]
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29 qryEnd = data[4]
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30 score = data[5]
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31 strand = data[6]
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32 frame = data[7]
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33 attributes = data[8][:-1].split()
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34
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35 sbjName = attributes[1]
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36 sbjStart = attributes[2]
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37 sbjEnd = attributes[3][:-1]
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38 percId = (1 - float(attributes[-1])) * 100.0
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39
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40 if strand != "+":
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41 tmp = sbjStart
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42 sbjStart = sbjEnd
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43 sbjEnd = tmp
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44
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45 if self._removeSameSequences \
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46 and "chunk" in qryName and "chunk" in sbjName \
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47 and min(int(qryStart), int(qryEnd)) == 1 \
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48 and min(int(sbjStart), int(sbjEnd)) == 1 \
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49 and percId == 100.0:
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50 line = self.inFile.readline()
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51 continue
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52
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53 if qryStart < qryEnd:
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54 alignLine = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, "0.0", score, percId)
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55 else:
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56 alignLine = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (qryName, qryEnd, qryStart, sbjName, sbjEnd, sbjStart, "0.0", score, percId)
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57
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58 tmpFile.write(alignLine)
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59
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60 file.close()
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61 tmpFile.close()
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62
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63 os.system("sort -k 1,1 -k 4,4 -k 2,2n -k 3,3n -k 5,5n -k 6,6n -k 8,8n %s > %s" % (tmpFileName, self._outputAlignFileName))
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64 os.remove(tmpFileName)
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65
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66
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