# <codecell>
from itertools import product
list(product('abcdefg', range(5)))
# <codecell>
fields = ['Name','RegionName', 'QueryNucStart','QueryNucStop','QueryNuc',
'RegionNucStart','RegionNucStop','RegionAAStart', 'RegionAAStop', 'QueryAA']
with open('TestData/LocatorRes.tsv', 'w') as handle:
writer = csv.DictWriter(handle, fields, delimiter='\t')
writer.writeheader()
for row in process_seqs(input_seqs, extract_regions = True):
writer.writerow(row)
#print row
#raise KeyError
# <codecell>
import csv
headers = ['Name', 'RegionName', 'QueryNucStart', 'QueryNucStop', 'QueryNuc',
'RegionNucStart', 'RegionNucStop', 'RegionAAStart','RegionAAStop','QueryAA']
with open('test_output.tsv', 'w') as handle:
writer = csv.DictWriter(handle, headers, delimiter='\t')
found_pats = set()
# <codecell>
!/home/will/staden-2.0.0b9.x86_64/bin/convert_trace --help
# <codecell>
res = call_muscle(seqs)
with open('align_data.fasta', 'w') as handle:
fasta_writer(handle, res)
# <codecell>
from HIVTransTool import process_seqs
results = list(process_seqs(seqs[:50], extract_regions = True, known_names = 50))
# <codecell>
for row in results:
if row['RegionName'] == 'LTR5':
print row['Name'], row['QueryNuc']
# <codecell>
results[:5]
# <codecell>