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1 #!/usr/bin/env python
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2
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3 import sys
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4 import getopt
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5
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6
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7 def help():
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8 print
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9 print "usage: blast2align.py [ options ]"
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10 print "options:"
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11 print " -h: this help"
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12 print " -i: input file name (format=tabulated BLAST)"
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13 print " -o: output file name (format=align, default=inFileName+'.align')"
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14 print
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15
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16
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17 def blast2align( inFile, outFile ):
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18 inFileHandler = open( inFile, "r" )
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19 outFileHandler = open( outFile, "w" )
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20 while True:
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21 line = inFileHandler.readline()
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22 if line == "":
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23 break
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24 if line[0] != "#":
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25 data = line.split("\t")
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26 qryName = data[0]
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27 sbjName = data[1]
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28 percId = data[2]
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29 qryStart = data[6]
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30 qryEnd = data[7]
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31 sbjStart = data[8]
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32 sbjEnd = data[9]
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33 Eval = data[10]
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34 bitScore = data[11][:-1]
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35 string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, Eval, bitScore, percId )
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36 outFileHandler.write( string )
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37 inFileHandler.close()
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38 outFileHandler.close()
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39
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40
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41 def main():
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42 inFileName = ""
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43 outFileName = ""
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44
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45 try:
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46 opts, args = getopt.getopt(sys.argv[1:],"hi:o:")
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47 except getopt.GetoptError, err:
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48 sys.stderr.write( "%s\n" % str(err) )
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49 help()
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50 sys.exit(1)
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51 for o,a in opts:
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52 if o == "-h":
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53 help()
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54 sys.exit(0)
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55 elif o == "-i":
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56 inFileName = a
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57 elif o == "-o":
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58 outFileName = a
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59
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60 if inFileName == "":
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61 msg = "ERROR: missing input file name (-i)"
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62 sys.stderr.write( "%s\n" % msg )
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63 help()
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64 sys.exit(1)
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65
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66 if outFileName == "":
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67 outFileName = inFileName + ".align"
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68
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69 blast2align( inFileName, outFileName )
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70
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71 return 0
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72
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73
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74 if __name__ == "__main__":
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75 main()
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