biocore / biocore/microprot

BUG: split_search.mask_sequence does not pick optimal fragments

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#51 3 comments 0 reactions 1 assignee Claimed by @sjanssen2 View on GitHub
bug
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Description

example HHsearch output:
```
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1W36_D EXODEOXYRIBONUCLEASE V 97.3 1.1E-06 2.1E-11 82.9 0.0 31 149-181 152-182 (608)
2 2P65_A Hypothetical protein PF 97.3 1.5E-06 2.7E-11 63.7 0.0 21 162-182 42-62 (187)
3 1W4R_A THYMIDINE KINASE (E.C.2 97.2 1.6E-06 3E-11 71.1 0.0 22 160-181 17-38 (195)
4 3B85_B Phosphate starvation-in 97.2 1.8E-06 3.3E-11 63.6 0.0 20 163-182 22-41 (208)
5 2ZPA_B Uncharacterized protein 97.2 2.3E-06 4.1E-11 87.2 0.0 138 162-343 191-341 (671)
6 3E1S_A Exodeoxyribonuclease V, 97.1 2.8E-06 5.1E-11 80.4 0.0 31 150-182 193-223 (574)
7 3GP8_A Exodeoxyribonuclease V, 97.1 2.8E-06 5.1E-11 80.4 0.0 31 150-182 193-223 (574)
8 5FTF_A TPR DOMAIN PROTEIN (E.C 97.1 3.8E-06 6.9E-11 73.1 0.0 21 162-182 20-40 (433)
9 3WHK_A Proteasome-activating n 97.1 4E-06 7.2E-11 64.0 0.0 23 161-183 49-71 (270)
10 3WHK_H Proteasome-activating n 97.1 4E-06 7.2E-11 64.0 0.0 23 161-183 49-71 (270)
11 5FTB_A TPR DOMAIN PROTEIN (E.C 97.1 4.2E-06 7.6E-11 72.8 0.0 21 162-182 20-40 (433)
12 2B8T_D Thymidine kinase (E.C.2 97.0 4.6E-06 8.3E-11 70.8 0.0 23 159-181 8-30 (223)
13 2B8T_A Thymidine kinase (E.C.2 97.0 4.6E-06 8.3E-11 70.8 0.0 23 159-181 8-30 (223)
14 4UXH_B THYMIDINE KINASE (E.C.2 97.0 5E-06 9E-11 66.0 0.0 22 161-182 3-24 (184)
15 4UXH_A THYMIDINE KINASE (E.C.2 97.0 5E-06 9E-11 66.0 0.0 22 161-182 3-24 (184)
16 5FHH_B ATP-dependent DNA helic 97.0 5.2E-06 9.3E-11 73.6 0.0 19 163-181 22-40 (442)
17 5FHH_A ATP-dependent DNA helic 97.0 5.2E-06 9.3E-11 73.6 0.0 19 163-181 22-40 (442)
18 5FUV_A THYMDINE KINASE (E.C.2. 97.0 5.2E-06 9.4E-11 64.9 0.0 21 162-182 2-22 (182)
19 5FUW_A THYMDINE KINASE (E.C.2. 97.0 5.2E-06 9.4E-11 64.9 0.0 21 162-182 2-22 (182)
20 3VKW_A Replicase large subunit 96.9 7.7E-06 1.4E-10 77.3 0.0 95 161-262 159-275 (446)
21 3UPU_A ATP-dependent DNA helic 96.9 8.4E-06 1.5E-10 73.4 0.0 46 118-181 18-63 (459)
22 5EQT_A Proteasome-activating n 96.8 1.6E-05 2.9E-10 60.3 0.0 24 161-184 37-60 (257)
23 5LD2_D RecBCD enzyme subunit R 96.8 1.7E-05 3.1E-10 76.5 0.0 31 149-181 153-183 (609)
24 2J87_B THYMIDINE KINASE (E.C.2 96.7 1.7E-05 3.1E-10 62.0 0.0 21 162-182 3-23 (177)
25 2J87_D THYMIDINE KINASE (E.C.2 96.7 1.7E-05 3.1E-10 62.0 0.0 21 162-182 3-23 (177)
26 1JBK_A CLPB PROTEIN; Beta barr 96.7 1.9E-05 3.4E-10 58.2 0.0 22 161-182 41-62 (195)
27 4N0N_A Replicase polyprotein 1 96.7 2E-05 3.6E-10 74.7 0.0 37 214-260 254-290 (423)
```

from this, `mask_sequence` picks:
```
>NZ_stefan.1_22_149-181 # PDB # 1 # 2017-07-01 18:20:24
>NZ_stefan.1_22_214-260 # PDB # 1 # 2017-07-01 18:20:24
```
with parameters:
```
min_prob: 95
min_fragment_length: 10
```

However, it should pick `2ZPA_B 162-343` (hit 5), as it is the longest fragment overlapping with shorter picks.
It looks like HHsearch error, but it's something we could account for.

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