Sebastian Kurscheid skurscheid
skurscheid
/ isPairedSRA.py
Created
March 29, 2020 23:30
— forked from deto/isPairedSRA.py
Function to determine if an SRA file has paired or single-ended reads
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| def isPairedSRA(filename): | |
| filename = os.path.abspath(filename); | |
| try: | |
| contents = sp.check_output(["fastq-dump","-X","1","-Z","--split-spot", filename]); | |
| except sp.CalledProcessError, e: | |
| raise Exception("Error running fastq-dump on",filename); | |
| if(contents.count("\n") == 4): | |
| return False; | |
| elif(contents.count("\n") == 8): |