Python program that reads a fastq file and calculate Phred score

Question

[sherrygeek]

Hi!

I need help with solving the following question with Python3:

Write a Python program that reads a fastq file and calculate how many bases have Phred base read quality of zero, between 1 and 10 (inclusive), 11 and 20, 21 and 30, 31 and 40, and above 40.

The final results should be like:

Base quality zero: XXX bases

Base quality 1-10: YYY bases

Base quality 11-20: ZZZ bases

Base quality 21-30: QQQ bases

Base quality 31-40: RRR bases

Base quality above 40: SSS bases

I don't know where to start. Any help will be greatly appreciated!

[sherrygeek]

And I know the post Python 3: Only Look at Quality Line. Still having difficulties.

[swbarnes2]

No one wants to write your program for you. If you really want help, post your code, and people will probably be be to see why it's not working.

Answer 1

[Istvan Albert]

To decode a base quality of say character I can use the formula ord("I") - 33

 qual = ord("I") - 33
 print (qual)

prints the Phred quality for character I as

40

to apply this to multiple codes, put it into a function:

def decode(c):
    return ord(c) - 33

letters = "II93882$%@%%@"

values = map(decode, letters)
values = list(values)

print (values)

prints:

[40, 40, 24, 18, 23, 23, 17, 3, 4, 31, 4, 4, 31]

this should be sufficient to get your started

[sherrygeek]

Thank you so much!!!!