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Fixes issue tkzeng/Pangolin#13 #21

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Fixes issue tkzeng/Pangolin#13 #21

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9 changes: 6 additions & 3 deletions pangolin/pangolin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,16 +16,19 @@


def one_hot_encode(seq, strand):
seq = seq.upper().replace('A', '1').replace('C', '2')
seq = seq.replace('G', '3').replace('T', '4').replace('N', '0')
# Convert to uppercase
seq = seq.upper()
# Replace every character that is not A, C, G, or T with 'N'
seq = ''.join(['N' if char not in 'ACGT' else char for char in seq])
# Then replace A, C, G, T with 1, 2, 3, 4, respectively, and N (everything else) with 0
seq = seq.replace('A', '1').replace('C', '2').replace('G', '3').replace('T', '4').replace('N', '0')
if strand == '+':
seq = np.asarray(list(map(int, list(seq))))
elif strand == '-':
seq = np.asarray(list(map(int, list(seq[::-1]))))
seq = (5 - seq) % 5 # Reverse complement
return IN_MAP[seq.astype('int8')]


def compute_score(ref_seq, alt_seq, strand, d, models):
ref_seq = one_hot_encode(ref_seq, strand).T
ref_seq = torch.from_numpy(np.expand_dims(ref_seq, axis=0)).float()
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