def test_seq_align_to_ref_multi():
ref_seq = 'ATCGATTGC'
test_seq = 'ATCGATGC'
cor_mapping = 'ATCGA-TGC'
inp = [('test1', test_seq)] * 10
res = list(GeneralSeqTools.seq_align_to_ref(inp, ref_seq, max_workers=5))
result = [('test1', cor_mapping)] * 10
eq_(res, result)
GGAGTGGtcaaCCCtCaGatGctgCATATAAGCagcTGCTTTtcgcctgt
actgggtctctctaggtagaccagatctgagcctgggagctctctggcta
tctagggaacccactgcttaagcctcaataaagcttgccttgagtgctct
aagtagtgtgtgccctctgttttgactctggtaactagagatccctcaga
cccttttggtagtgaggaaatctctagca""".replace('\n', '').upper()
ltrs = {'B':conb_ltr, 'C':conc_ltr}
# <codecell>
ltr_aligns = []
for align_sub, ltr_seq in ltrs.items():
for sub, df in pseqdf.groupby(level = 'Subtype'):
ltr_seqs = [(gi, seq) for (_, gi), seq in df['ltr'].dropna().to_dict().items()]
for num, (gi, align) in enumerate(GeneralSeqTools.seq_align_to_ref(ltr_seqs, ltr_seq)):
if (num == 0) or (num == 100) or (num == 10) or (num % 1000 == 0):
print align_sub, sub, num
ltr_aligns.append({
'Subtype':sub,
'ID':gi,
'Align-Con'+align_sub:align
})
# <codecell>
ltr_align_df = pd.pivot_table(pd.DataFrame(ltr_aligns),
rows = ['Subtype', 'ID'],
values = ['Align-ConC', 'Align-ConB'],
aggfunc = 'first')
