pyfastaq/sequences.py
def contig_coords(self):
        '''Finds coords of contigs, i.e. everything that's not a gap (N or n). Returns a list of Intervals. Coords are zero-based'''
        # contigs are the opposite of gaps, so work out the coords from the gap coords
        gaps = self.gaps()

        if len(gaps) == 0:
            return [intervals.Interval(0, len(self) - 1)]

        coords = [0]
        for g in gaps:
            if g.start == 0:
                coords = [g.end + 1]
            else:
                coords += [g.start - 1, g.end + 1]

        if coords[-1] < len(self):
            coords.append(len(self) - 1)

        return [intervals.Interval(coords[i], coords[i+1]) for i in range(0, len(coords)-1,2)]
def contig_coords(self):
        '''Finds coords of contigs, i.e. everything that's not a gap (N or n). Returns a list of Intervals. Coords are zero-based'''
        # contigs are the opposite of gaps, so work out the coords from the gap coords
        gaps = self.gaps()

        if len(gaps) == 0:
            return [intervals.Interval(0, len(self) - 1)]

        coords = [0]
        for g in gaps:
            if g.start == 0:
                coords = [g.end + 1]
            else:
                coords += [g.start - 1, g.end + 1]

        if coords[-1] < len(self):
            coords.append(len(self) - 1)

        return [intervals.Interval(coords[i], coords[i+1]) for i in range(0, len(coords)-1,2)]
def contig_coords ( self ) : # contigs are the opposite of gaps, so work out the coords from the gap coords gaps = self . gaps ( ) if len ( gaps ) == 0 : return [ intervals . Interval ( 0 , len ( self ) - 1 ) ] coords = [ 0 ] for g in gaps : if g . start == 0 : coords = [ g . end + 1 ] else : coords += [ g . start - 1 , g . end + 1 ] if coords [ - 1 ] < len ( self ) : coords . append ( len ( self ) - 1 ) return [ intervals . Interval ( coords [ i ] , coords [ i + 1 ] ) for i in range ( 0 , len ( coords ) - 1 , 2 ) ]
Finds coords of contigs, i.e. everything that's not a gap (N or n). Returns a list of Intervals. Coords are zero-based
Finds coords of contigs i . e . everything that s not a gap ( N or n ) . Returns a list of Intervals . Coords are zero - based