ltr_seqs += list(fasta_reader(handle))
print len(ltr_seqs)
# <codecell>
conb_ltr = """TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAA
GGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGC
TAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCA
TGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAG
CTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGC
GTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTC
TCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCC
TTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTG
TGGAAAATCTCT""".replace('\n', '')
ltr_align = list(seq_align_to_ref(ltr_seqs, conb_ltr, max_workers = 20))
# <codecell>
ltr_bin_align = []
align_inds = []
for key, seq in ltr_align:
align_inds.append(tuple(key.split('-')))
hit_first = False
bins = []
for g, cb in zip(seq, conb_ltr):
if ~hit_first and (g == '-'):
bins.append(np.nan)
continue
hit_first = True
bins.append(1.0 if g==cb else 0.0)
oseqs = []
if os.path.exists('aligned_seq.pkl'):
with open('aligned_seq.pkl') as handle:
oseqs = pickle.load(handle)
else:
for f in files:
fname = f.rsplit(os.sep,1)[-1].split('.')[0]
parts = fname.split('-')
prot_name = parts[1].replace('_','-')
if prot_name == 'V3':
continue
with open(f) as handle:
prot_seqs = list(trans_seq(handle, set(trop_data.index), trans=prot_name != 'LTR'))
print prot_name, len(prot_seqs)
aligned_seqs = seq_align_to_ref(prot_seqs, ref_seqs[prot_name], max_workers=20)
for name, seq in aligned_seqs:
oseqs.append({
'Accession':name,
'Seq':seq,
'Prot':prot_name
})
# <codecell>
aligned_seqs = pd.pivot_table(pd.DataFrame(oseqs),
rows='Accession',
cols='Prot',
values='Seq',
aggfunc='first')
------------AGCTGCATCCGGAGTACTTC---------AAGAACTGCT-----------------------------
-------GACATCGA------------------------GCTTG---CT----------------------ACAA---GG
GACTTTCCGCTGGGGACTTTCCAG-------------GGAGGCGTGGCCTGGGCGGGACT---GGGGAGTGGCGA---GC
CCTCAGATCCTGCATATAAGCAGC---TGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAG
CTCTCTGGCT---AACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCT---TGAGTGCTTC---AAGTAGTGTG
TGC---CCGTCTG---TTGTGTGACTCTGGT---AACTAGAGATCCC---TCAGAC---CCT---TTTAGTCAGTGTGG-
--AAAATCTCT""".replace(
"\n", ""
).replace(
"-", ""
)
# <codecell>
aln_seqs = []
for gi, aln_seq in seq_align_to_ref(ltr_seqs, hxb2, max_workers=50):
try:
aln_seqs.append((gi2date[gi], aln_seq))
except KeyError:
pass
# <codecell>
sorted_alns = sorted(aln_seqs, key=lambda x: x[0])
# <codecell>
from itertools import groupby
from collections import defaultdict
found_seqs = set()
