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Question

So I'm trying to parce a FastQ sequence, but I'm a beginner to Python, and I'm a little confused as to how to complete my code. This is what the program is supposed to carry out:

if I enter the FASTQ seqname line...

@EAS139:136:FC706VJ:2:2104:15343:197393

...then the program will output:

Instrument = EAS139
Run ID = 136
Flow Cell ID = FC706VJ
Flow Cell Lane = 2
Tile Number = 2104
X-coord = 15343
Y-coord = 197393

Here's my (incomplete) code:

    class cleaner:
    def __init__(self,str):
        self.str = seq.upper()
    def line (self):
        1 = inStr.replace ('@',' ').replace (':',' ').split (' ')
newTuple =(float(1[1]),float(1[2))] #...etc                


    def printInstrument (self):
        print ("Instrument: {0}".format(float(1[1])))
    def printRunID (self):
        print ("Run ID: {0}".format(float(1[2])))
    def printFlowCellID (self):
        print ("Flow Cell ID: {0}".format(float(1[3])))
    def printFlowCellLane (self):
        print ("Flow Cell Lane: {0}".format(float(1[4])))
    def printTileNumber (self):
        print ("Tile Number{0}".format(float(1[5])))
    def printX (self):
        print ("X-coordinate:{0}".format(float(1[6])))
    def printY (self):
        print ("y-coordinate: {0}".format(float(1[7])))
 def main():
    seq = input('Enter FastQ sequence:')


main()

Answer 1

If your input is like that, remove the first character (the @ ), split the string by : and then zip the values you'll obtain by doing that to a pre-set of keys:

>>> keys=["Instrument", "Run ID", "Flow Cell ID", "Flow Cell Lane", "Title Number", "X-coord", "Y-coord"]
>>> values="@EAS139:136:FC706VJ:2:2104:15343:197393"[1:].split(':')
>>> my_dict=dict(zip(keys, values))
>>> for key, val in my_dict.iteritems():
...     print "%s: %s" % (key, val)
...
Run ID: 136
Flow Cell ID: FC706VJ
Title Number: 2104
Y-coord: 197393
X-coord: 15343
Flow Cell Lane: 2
Instrument: EAS139

I strongly recommend that you check:

• Slicing strings ( here )
• What the split function does to an string
• What a dict is ( here )
• What zip does ( here )