def _next(self, line):
        if line.startswith('#'):
            return
    
        ge = GenomeElement(self._genome)
        cols = line.split('\t')
        
        if self._numCols is not None:
            if len(cols) != self._numCols:
                raise InvalidFormatError('Error: BED files must have the same number of columns in each data line.')
        else:
            self._numCols = len(cols)
            
        if self._numCols < self.MIN_NUM_COLS or self._numCols > self.MAX_NUM_COLS:
            raise InvalidFormatError('Error: BED file must contain between %s and %s columns.' % (self.MIN_NUM_COLS, self.MAX_NUM_COLS))

        ge.chr = self._checkValidChr(cols[0])
        ge.start = self._checkValidStart(ge.chr, int(cols[1]))
        
        self._parseEnd( ge, self._checkValidEnd(ge.chr, int(cols[2]), start=ge.start))
        self._parseName( ge, cols )
        self._parseVal( ge, cols )
        
        if self._numCols >= 6:
            ge.strand = self._getStrandFromString(cols[5])
        
        for i,extraCol in enumerate(self.BED_EXTRA_COLUMNS):
            if self._numCols >= i+7:
                setattr(ge, extraCol, cols[i+6])
        
        return ge
Example #2
0
    def _next(self, line):
        if line.startswith('#'):
            return

        ge = GenomeElement(self._genome)
        cols = line.split('\t')

        if self._numCols is not None:
            if len(cols) != self._numCols:
                raise InvalidFormatError(
                    'Error: BED files must have the same number of columns in each data line.'
                )
        else:
            self._numCols = len(cols)

        if self._numCols < self.MIN_NUM_COLS or self._numCols > self.MAX_NUM_COLS:
            raise InvalidFormatError('Error: BED file contains %s columns, but must contain between %s and %s columns.' \
                % (self._numCols, self.MIN_NUM_COLS, self.MAX_NUM_COLS))

        ge.chr = self._checkValidChr(cols[0])
        ge.start = self._checkValidStart(ge.chr, int(cols[1]))

        self._parseEnd(
            ge, self._checkValidEnd(ge.chr, int(cols[2]), start=ge.start))
        self._parseName(ge, cols)
        self._parseVal(ge, cols)

        if self._numCols >= 6:
            ge.strand = self._getStrandFromString(cols[5])

        for i, extraCol in enumerate(self.BED_EXTRA_COLUMNS):
            if self._numCols >= i + 7:
                setattr(ge, extraCol, cols[i + 6])

        return ge
    def _next(self, line):
        if len(line)>0 and line[0]=='#':
            return None
        
        origCols = line.split('\t')
        cols = [unquote(x) for x in origCols]
        
        if len(cols) != 9:
            raise InvalidFormatError("Error: GFF files must contain 9 tab-separated columns")

        ge = GenomeElement(self._genome)
        ge.chr = self._checkValidChr(cols[0])
        ge.source = cols[1]
        ge.type = cols[2]
        ge.start = self._checkValidStart(ge.chr, int(cols[3]) - 1)
        ge.end =  self._checkValidEnd(ge.chr, int(cols[4]), start=ge.start)
        ge.val = numpy.float(self._handleNan(cols[5]))
        ge.strand = self._getStrandFromString(cols[6])
        ge.phase = cols[7]
        ge.attributes = cols[8]
        
        for attr in origCols[8].split(';'):
            attrSplitted = attr.split('=')
            if len(attrSplitted) == 2:
                key, val = attrSplitted
                if key.lower() == 'id':
                    ge.id = unquote(val)
                elif key.lower() == 'name':
                    ge.name = unquote(val)
                
        return ge
Example #4
0
    def _next(self, line):
        cols = line.split('\t')

        ge = GenomeElement(self._genome)
        ge.chr = self._checkValidChr(cols[0])
        ge.start = int(cols[1])
        ge.end = int(cols[2])
        self._parseVal(ge, cols[3])

        return ge
 def _next(self, line):
     cols = line.split('\t')
     
     ge = GenomeElement(self._genome)
     ge.chr = self._checkValidChr(cols[0])
     ge.start = int(cols[1])
     ge.end = int(cols[2])
     self._parseVal(ge, cols[3])
     
     return ge
Example #6
0
    def _next(self, line):
        if line.startswith('##FASTA'):
            raise StopIteration

        if len(line) > 0 and line[0] == '#':
            return None

        origCols = line.split('\t')
        cols = [unquote(x) for x in origCols]

        if len(cols) != 9:
            raise InvalidFormatError(
                "Error: GFF files must contain 9 tab-separated columns")

        ge = GenomeElement(self._genome)
        ge.chr = self._checkValidChr(cols[0])
        ge.source = cols[1]

        self._parseThirdCol(ge, cols[2])

        ge.start = self._checkValidStart(ge.chr, int(cols[3]) - 1)
        ge.end = self._checkValidEnd(ge.chr, int(cols[4]), start=ge.start)

        self._parseSixthCol(ge, cols[5])

        ge.strand = self._getStrandFromString(cols[6])
        ge.phase = cols[7]
        ge.attributes = cols[8]

        for attr in origCols[8].split(';'):
            attrSplitted = attr.split('=')
            if len(attrSplitted) == 2:
                key, val = attrSplitted
                if key.lower() == 'id':
                    ge.id = unquote(val)
                elif key.lower() == 'name':
                    ge.name = unquote(val)

        return ge