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compute GC fraction from genbank (automate the process for other organisms) #12

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yseif opened this issue Aug 23, 2017 · 0 comments
Open

compute GC fraction from genbank (automate the process for other organisms) #12

yseif opened this issue Aug 23, 2017 · 0 comments

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@yseif
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yseif commented Aug 23, 2017

def getGC_content(genbank_file):
for seqrecord in SeqIO.parse(genbank_file, 'genbank'):
sequence = str(seqrecord.seq)
GC_fraction = (sequence.count('G')+sequence.count('C'))/float(sequence.count('G')+sequence.count('C')+sequence.count('T')+sequence.count('A'))
return GC_fraction
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