Entering edit mode
6.2 years ago
tim.ivanov.92
▴
40
How to retrieve target sequence from exonerate output?
from Bio import SearchIO
qresult = SearchIO.read('my_input', 'exonerate-text')
hit=qresult.hits
print hit[0].hsps[0]
and i get a list of coordinates
# Span Query range Hit range --- -------------- ---------------------- ---------------------- 0 208 [0:208] [12722276:12722484] 1 1512 [208:1720] [12722558:12724070] 2 138 [1720:1858] [12724205:12724343] 3 147 [1858:2005] [12724471:12724618] 4 85 [2005:2090] [12725711:12725796] 5 820 [2090:2910] [12725858:12726678] 6 371 [2910:3281] [12726745:12727116] 7 221 [3281:3502] [12729184:12729405] 8 218 [3502:3720] [12737958:12738176] 9 507 [3720:4227] [12738240:12738747] 10 382 [4227:4609] [12738806:12739188] 11 828 [4609:5437] [12743979:12744807]
But i can't find an option to retrieve the whole target sequence, is there a way to do this?