()
| 196 | |
| 197 | @report |
| 198 | def testDigestionTutorial(): |
| 199 | |
| 200 | print("testDigestionTutorial") |
| 201 | dig = ProteaseDigestion() |
| 202 | dig.getEnzymeName() # Trypsin |
| 203 | bsa = b'DEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVVSTQTALA' |
| 204 | bsa = AASequence.fromString(bsa) |
| 205 | result = [] |
| 206 | dig.digest(bsa, result) |
| 207 | print(result[4]) |
| 208 | len(result) # 74 peptides |
| 209 | assert len(result) == 74 |
| 210 | |
| 211 | names = [] |
| 212 | ProteaseDB().getAllNames(names) |
| 213 | len(names) # 25 by default |
| 214 | e = ProteaseDB().getEnzyme('Lys-C') |
| 215 | e.getRegExDescription() |
| 216 | e.getRegEx() |
| 217 | |
| 218 | dig = ProteaseDigestion() |
| 219 | dig.setEnzyme('Lys-C') |
| 220 | result = [] |
| 221 | dig.digest(bsa, result) |
| 222 | print(result[4]) |
| 223 | len(result) # 53 peptides |
| 224 | assert len(result) == 53 |
| 225 | |
| 226 | def gaussian(x, mu, sig): |
| 227 | import numpy as np |
nothing calls this directly
no test coverage detected