Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/PathNum2Id.py @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children |
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| 5:ea3082881bf8 | 6:769e306b7933 |
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| 1 class PathNum2Id( object ): | |
| 2 | |
| 3 def __init__(self): | |
| 4 self._inFileName = None | |
| 5 self._outFileName = None | |
| 6 | |
| 7 def setInFileName(self, fileName): | |
| 8 self._inFileName = fileName | |
| 9 | |
| 10 def setOutFileName(self, fileName): | |
| 11 self._outFileName = fileName | |
| 12 | |
| 13 def run( self ): | |
| 14 """ | |
| 15 Adapt the path IDs as the input file is the concatenation of several 'path' files. | |
| 16 """ | |
| 17 self._inFile = open( self._inFileName, "r" ) | |
| 18 self._outFile = open( self._outFileName, "w" ) | |
| 19 lines = self._inFile.readlines() | |
| 20 dID2count = {} | |
| 21 count = 1 | |
| 22 for line in lines: | |
| 23 if line == "": | |
| 24 break | |
| 25 strippedLine = line.strip('\n') | |
| 26 data = strippedLine.split("\t") | |
| 27 path = data[0] | |
| 28 qryName = data[1] | |
| 29 qryStart = int(data[2]) | |
| 30 qryEnd = int(data[3]) | |
| 31 sbjName = data[4] | |
| 32 sbjStart = int(data[5]) | |
| 33 sbjEnd = int(data[6]) | |
| 34 BLAST_Eval = data[7] | |
| 35 BLAST_score = data[8] | |
| 36 percId = data[9] | |
| 37 key_id = path + "-" + qryName + "-" + sbjName | |
| 38 if key_id not in dID2count.keys(): | |
| 39 newPath = count | |
| 40 count += 1 | |
| 41 dID2count[ key_id ] = newPath | |
| 42 else: | |
| 43 newPath = dID2count[ key_id ] | |
| 44 cmd = "%i\t%s\t%i\t%i\t%s\t%i\t%i\t%s\t%s\t%s\n" % ( newPath, qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, BLAST_Eval, BLAST_score, percId ) | |
| 45 self._outFile.write( cmd ) | |
| 46 self._inFile.close() | |
| 47 self._outFile.close() |