annotate smart_toolShed/commons/core/parsing/PathNum2Id.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

class PathNum2Id( object ):

    def __init__(self):
        self._inFileName = None
        self._outFileName = None

    def setInFileName(self, fileName):  
        self._inFileName = fileName  
        
    def setOutFileName(self, fileName):  
        self._outFileName = fileName        
        
    def run( self ):
        """
        Adapt the path IDs as the input file is the concatenation of several 'path' files.
        """
        self._inFile = open( self._inFileName, "r" )
        self._outFile = open( self._outFileName, "w" )
        lines = self._inFile.readlines()
        dID2count = {}
        count = 1
        for line in lines:
            if line == "":
                break
            strippedLine = line.strip('\n')
            data = strippedLine.split("\t")
            path = data[0]
            qryName = data[1]
            qryStart = int(data[2])
            qryEnd = int(data[3])
            sbjName = data[4]
            sbjStart = int(data[5])
            sbjEnd = int(data[6])
            BLAST_Eval = data[7]
            BLAST_score = data[8]
            percId = data[9]
            key_id = path + "-" + qryName + "-" + sbjName
            if key_id not in dID2count.keys():
                newPath = count
                count += 1
                dID2count[ key_id ] = newPath
            else:
                newPath = dID2count[ key_id ]
            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 )
            self._outFile.write( cmd )
        self._inFile.close()
        self._outFile.close()