Is there a python program where I can put in a fastq file and the output will be all of the quality scores
Biopython would be the robust way to handle this.
Since the quality scores are every 4th line starting from the 4th line, you could just use sed.
sed -n '4~4p' input.fastq
A Python program that prints out qualities could be as simple as:
stream = open("reads.fq")
for line in stream:
Though the sed answer by rpolicastro is probably the way to go
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