Python2 changes...

import serial
import Adafruit_BBIO.UART as UART
from time import sleep

UART.setup("UART2")
ser=serial.Serial("/dev/ttyS2", 9600)

class GPS:

    def __init__(self):
        #This sets up variables for useful commands.
        #This set is used to set the rate the GPS reports
        UPDATE_10_sec=  "$PMTK220,10000*2F\r\n" #Update Every 10 Seconds
        UPDATE_5_sec=  "$PMTK220,5000*1B\r\n"   #Update Every 5 Seconds
        UPDATE_1_sec=  "$PMTK220,1000*1F\r\n"   #Update Every One Second
        UPDATE_200_msec=  "$PMTK220,200*2C\r\n" #Update Every 200 Milliseconds
        #This set is used to set the rate the GPS takes measurements
        MEAS_10_sec = "$PMTK300,10000,0,0,0,0*2C\r\n" #Measure every 10 seconds
        MEAS_5_sec = "$PMTK300,5000,0,0,0,0*18\r\n"   #Measure every 5 seconds
        MEAS_1_sec = "$PMTK300,1000,0,0,0,0*1C\r\n"   #Measure once a second
        MEAS_200_msec= "$PMTK300,200,0,0,0,0*2F\r\n"  #Meaure 5 times a seconds
        #Set the Baud Rate of GPS
        BAUD_57600 = "$PMTK251,57600*2C\r\n"          #Set Baud Rate at 57600
        BAUD_9600 ="$PMTK251,9600*17\r\n"             #Set 9600 Baud Rate
        #Commands for which NMEA Sentences are sent
        ser.write(BAUD_57600)
        sleep(1)
        ser.baudrate=57600
        GPRMC_ONLY= "$PMTK314,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0*29\r\n" #Send only the GPRMC Sentence
        GPRMC_GPGGA="$PMTK314,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0*28\r\n"#Send GPRMC AND GPGGA Sentences
        SEND_ALL ="$PMTK314,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0*28\r\n" #Send All Sentences
        SEND_NOTHING="$PMTK314,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0*28\r\n" #Send Nothing
        ser.write(UPDATE_1_sec)
        sleep(1)
        ser.write(MEAS_1_sec)
        sleep(1)
        ser.write(GPRMC_GPGGA)
        sleep(1)
        ser.flushInput()
        ser.flushInput()

    def read(self):
        ser.flushInput()
        ser.flushInput()
        while ser.inWaiting()==0:
            pass
        self.NMEA1=ser.readline()
        while ser.inWaiting()==0:
            pass
        self.NMEA2=ser.readline()
        NMEA1_array=self.NMEA1.split(',')
        NMEA2_array=self.NMEA2.split(',')
        if NMEA1_array[0]=='$GPRMC':
            self.timeUTC=NMEA1_array[1][:-8]+':'+NMEA1_array[1][-8:-6]+':'+NMEA1_array[1][-6:-4]
            self.latDeg=NMEA1_array[3][:-7]
            self.latMin=NMEA1_array[3][-7:]
            self.latHem=NMEA1_array[4]
            self.lonDeg=NMEA1_array[5][:-7]
            self.lonMin=NMEA1_array[5][-7:]
            self.lonHem=NMEA1_array[6]
            self.knots=NMEA1_array[7]
        if NMEA1_array[0]=='$GPGGA':
            self.fix=NMEA1_array[6]
            self.altitude=NMEA1_array[9]
            self.sats=NMEA1_array[7]
        if NMEA2_array[0]=='$GPRMC':
            self.timeUTC=NMEA2_array[1][:-8]+':'+NMEA1_array[1][-8:-6]+':'+NMEA1_array[1][-6:-4]
            self.latDeg=NMEA2_array[3][:-7]
            self.latMin=NMEA2_array[3][-7:]
            self.latHem=NMEA2_array[4]
            self.lonDeg=NMEA2_array[5][:-7]
            self.lonMin=NMEA2_array[5][-7:]
            self.lonHem=NMEA2_array[6]
            self.knots=NMEA2_array[7]

        if NMEA2_array[0]=='$GPGGA':
            self.fix=NMEA2_array[6]
            self.altitude=NMEA2_array[9]
            self.sats=NMEA2_array[7]

myGPS=GPS()
GPSdata=open('/root/GPS_data/GPS.txt', 'w')
GPSdata.close()
while(1):
    myGPS.read()
    if myGPS.fix!=0:
        try:
            latDec=float(myGPS.latDeg)+float(myGPS.latMin)/60.
            lonDec=float(myGPS.lonDeg)+float(myGPS.lonMin)/60.
            if myGPS.lonHem=='W':
                lonDec=(-1)*lonDec
            if myGPS.latHem=='S':
                latDec=(-1)*latDec
            alt=myGPS.altitude
            GPSdata=open('/root/GPS_data/GPS.txt', 'a')
            myString=str(lonDec)+','+str(latDec)+','+alt+' '
            GPSdata.write(myString)
            GPSdata.close()
        except:
            pass