In [1]:

    

import os
import os.path as osp

import pickle

from blast import *

from src.python.preprocess2 import *


    

    




/home/yotamfr/development/prot2vec/virtualenv/lib/python3.6/site-packages/Bio/SearchIO/__init__.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release.
  BiopythonExperimentalWarning)

In [2]:

    

def preds_by_attr(hits_per_uid, attr, func=lambda x: x):
    preds = {}
    pbar = tqdm(range(len(hits_per_uid)), desc="sequences processed")
    for uid, hits in hits_per_uid.items():
        pbar.update(1)
        if len(hits) == 0:
            continue
        preds[uid] = {}
        for go, hits in hits.items():
            hs =[getattr(h, attr) for h in hits if h.evalue < 0.001]
            if len(hs) == 0:
                continue
            preds[uid][go] = func(max(hs))
    pbar.close()
    return preds

def load_object(pth):
    with open(pth, 'rb') as f:
        loaded_dist_mat = pickle.load(f)
        assert len(loaded_dist_mat) > 0
    return loaded_dist_mat


    

In [3]:

    

pth_to_cco_hsps = "../../Data/cafapi_blast_CCO_hsp_p2v2"
pth_to_bpo_hsps = "../../Data/cafapi_blast_BPO_hsp_p2v2"

hits_cco_per_uid = load_object(pth_to_cco_hsps)
hits_bpo_per_uid = load_object(pth_to_bpo_hsps)

preds_cco_pident = preds_by_attr(hits_cco_per_uid, "pident", func=lambda x: x/100)
preds_bpo_pident = preds_by_attr(hits_bpo_per_uid, "pident", func=lambda x: x/100)


    

    




sequences processed: 100%|██████████| 18313/18313 [00:00<00:00, 19189.42it/s]
sequences processed: 100%|██████████| 18313/18313 [00:02<00:00, 7728.76it/s]

In [4]:

    

PATH = "../../Data/CAFA_PI/submission"

if not osp.exists(PATH):
    os.makedirs(PATH)


    

In [5]:

    

targets_by_sp = {"208963": load_targets("../../Data/CAFA_PI/targetFiles/target.208963.fasta"),
                 "237561": load_targets("../../Data/CAFA_PI/targetFiles/target.237561.fasta")}

len(targets_by_sp["208963"]), len(targets_by_sp["237561"]), sum(map(len, targets_by_sp.values()))


    

    




74%100%
Finished loading 5892 sequences!
100%
Finished loading 12421 sequences!






    
Out[5]:





(5892, 12421, 18313)

In [6]:

    

def get_go_dict(targets, preds_by_uid):
    go_dict = {}
    for uid in targets.keys():
        if uid not in preds_by_uid:
            continue
        for go, prob in preds_by_uid[uid].items():
            if go not in go_dict:
                go_dict[go] = [(uid, prob)]
            else:
                go_dict[go].append((uid, prob))
    return go_dict


    

In [13]:

    

num_model = 1
group_id = "yotamfr"
go_targets = {"GO:0001539": {
    "ancestors": ["GO:0048870", "GO:0040011", "GO:0051674", "GO:0006928"],
    "related": ["GO:0005929", "GO:0031514", "GO:0097589", "GO:0009288", "GO:0055040"]
}, "GO:0042710": {
    "ancestors": ["GO:0044764", "GO:0051704"],
    "related": ["GO:0097311", "GO:0097312", "GO:0097313", "GO:0044420", "GO:0031012", "GO:0044421", "GO:000576"]
}}
        

for sp in ["208963", "237561"]:
    go_cco_dict = get_go_dict(targets_by_sp[sp], preds_cco_pident)
    go_bpo_dict = get_go_dict(targets_by_sp[sp], preds_bpo_pident)
    
    for go in go_targets.keys():
        
        candidates = []
        if go in go_bpo_dict:
            for uid, prob in go_bpo_dict[go]:
                candidates.append((uid, prob))
                print(go, uid, prob)
        
        for anc in go_targets[go]["ancestors"]:
            if anc in go_bpo_dict:
                for uid1, prob1 in go_bpo_dict[anc]:
                    for rel in go_targets[go]["related"]:
                        if rel in go_cco_dict:
                            for uid2, prob2 in go_cco_dict[rel]:
                                if uid1 == uid2:
                                    candidates.append((uid1, max(prob1, prob2)))
                                    print(go, uid1, max(prob1, prob2))
                            
        _, go_id = go.split(":")

        lines = ["AUTHOR\t%s\n" % group_id, "MODEL\t%d\n" % num_model, "KEYWORDS\tsequence alignment, homolog, other functional information\n"]
        with open(osp.join(PATH, "%s_%d_%s_%s.txt" % (group_id, num_model, sp, go_id)), "w+") as f:
            for uid, prob in candidates:
                lines.append("%s\t%.2f\n" % (uid, prob))
            lines.append("END")
            f.writelines(lines)


    

    




GO:0001539 T2089630000610 0.33030000000000004
GO:0001539 T2089630000660 0.3333
GO:0001539 T2089630004698 0.31980000000000003
GO:0001539 T2089630000621 0.2789
GO:0001539 T2089630001139 0.4857
GO:0001539 T2089630001204 0.35369999999999996
GO:0001539 T2089630001225 0.3778
GO:0001539 T2089630001619 0.3195
GO:0001539 T2089630001694 0.3346
GO:0001539 T2089630002626 0.35350000000000004
GO:0001539 T2089630002956 0.3211
GO:0001539 T2089630004698 0.3506
GO:0001539 T2089630005007 0.2922
GO:0001539 T2089630005123 0.3423
GO:0001539 T2089630005598 0.285
GO:0001539 T2375610000271 0.26789999999999997
GO:0001539 T2375610000271 0.2667
GO:0001539 T2375610000272 0.26789999999999997
GO:0001539 T2375610000272 0.2667
GO:0001539 T2375610000368 0.2977
GO:0001539 T2375610000368 0.2944
GO:0001539 T2375610000369 0.2977
GO:0001539 T2375610000369 0.2944
GO:0001539 T2375610000516 0.3772
GO:0001539 T2375610000535 0.6082
GO:0001539 T2375610000535 0.2945
GO:0001539 T2375610000536 0.6082
GO:0001539 T2375610000536 0.2945
GO:0001539 T2375610000555 0.3492
GO:0001539 T2375610000555 0.3519
GO:0001539 T2375610000581 0.4696
GO:0001539 T2375610000581 0.4696
GO:0001539 T2375610000688 0.2764
GO:0001539 T2375610000689 0.2764
GO:0001539 T2375610000783 0.6118
GO:0001539 T2375610000783 0.6118
GO:0001539 T2375610000784 0.6118
GO:0001539 T2375610000784 0.6118
GO:0001539 T2375610001087 0.6846
GO:0001539 T2375610001087 0.33640000000000003
GO:0001539 T2375610001095 0.4531
GO:0001539 T2375610001095 0.4531
GO:0001539 T2375610001189 0.293
GO:0001539 T2375610001189 0.2784
GO:0001539 T2375610001190 0.293
GO:0001539 T2375610001190 0.2784
GO:0001539 T2375610001248 0.5088
GO:0001539 T2375610001249 0.5088
GO:0001539 T2375610001265 0.3492
GO:0001539 T2375610001265 0.3519
GO:0001539 T2375610001278 0.47
GO:0001539 T2375610001279 0.47
GO:0001539 T2375610001356 0.3235
GO:0001539 T2375610001356 0.31980000000000003
GO:0001539 T2375610001357 0.3204
GO:0001539 T2375610001357 0.31980000000000003
GO:0001539 T2375610001554 0.4389
GO:0001539 T2375610001555 0.4389
GO:0001539 T2375610001770 0.4146
GO:0001539 T2375610001770 0.4146
GO:0001539 T2375610001771 0.4146
GO:0001539 T2375610001771 0.4146
GO:0001539 T2375610001774 0.3464
GO:0001539 T2375610001774 0.2798
GO:0001539 T2375610001775 0.3464
GO:0001539 T2375610001775 0.2798
GO:0001539 T2375610001785 0.3931
GO:0001539 T2375610001785 0.3125
GO:0001539 T2375610001838 0.337
GO:0001539 T2375610001838 0.337
GO:0001539 T2375610001839 0.337
GO:0001539 T2375610001839 0.337
GO:0001539 T2375610001907 0.8579000000000001
GO:0001539 T2375610001929 0.31
GO:0001539 T2375610001929 0.3061
GO:0001539 T2375610001932 0.31
GO:0001539 T2375610001932 0.3061
GO:0001539 T2375610001938 0.2186
GO:0001539 T2375610001963 0.38530000000000003
GO:0001539 T2375610001963 0.3159
GO:0001539 T2375610001967 0.38530000000000003
GO:0001539 T2375610001967 0.3159
GO:0001539 T2375610001981 0.2845
GO:0001539 T2375610001981 0.3875
GO:0001539 T2375610002101 0.6315999999999999
GO:0001539 T2375610002101 0.289
GO:0001539 T2375610002164 0.344
GO:0001539 T2375610002164 0.344
GO:0001539 T2375610002188 0.5397
GO:0001539 T2375610002188 0.2692
GO:0001539 T2375610002189 0.5397
GO:0001539 T2375610002189 0.2692
GO:0001539 T2375610002363 0.3243
GO:0001539 T2375610002363 0.32270000000000004
GO:0001539 T2375610002364 0.3243
GO:0001539 T2375610002364 0.32270000000000004
GO:0001539 T2375610002412 0.344
GO:0001539 T2375610002412 0.344
GO:0001539 T2375610002573 0.3931
GO:0001539 T2375610002573 0.3125
GO:0001539 T2375610002805 0.33509999999999995
GO:0001539 T2375610002805 0.3299
GO:0001539 T2375610002808 0.33509999999999995
GO:0001539 T2375610002808 0.3299
GO:0001539 T2375610002935 0.2825
GO:0001539 T2375610002935 0.28
GO:0001539 T2375610002936 0.2825
GO:0001539 T2375610002936 0.28
GO:0001539 T2375610002978 0.3191
GO:0001539 T2375610002978 0.301
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GO:0001539 T2375610003047 0.5745
GO:0001539 T2375610003048 0.5745
GO:0001539 T2375610003048 0.5745
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GO:0001539 T2375610003056 0.26530000000000004
GO:0001539 T2375610003214 0.375
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GO:0001539 T2375610003244 0.25730000000000003
GO:0001539 T2375610003245 0.3116
GO:0001539 T2375610003245 0.25730000000000003
GO:0001539 T2375610003290 0.3651
GO:0001539 T2375610003290 0.35710000000000003
GO:0001539 T2375610003293 0.3651
GO:0001539 T2375610003293 0.35710000000000003
GO:0001539 T2375610003296 0.2981
GO:0001539 T2375610003296 0.2981
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GO:0001539 T2375610003297 0.2981
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GO:0001539 T2375610003330 0.4986
GO:0001539 T2375610003456 0.3131
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GO:0001539 T2375610003457 0.3131
GO:0001539 T2375610003457 0.2821
GO:0001539 T2375610003471 0.3295
GO:0001539 T2375610003472 0.3295
GO:0001539 T2375610003594 0.39289999999999997
GO:0001539 T2375610003594 0.3387
GO:0001539 T2375610003675 0.36729999999999996
GO:0001539 T2375610003676 0.36729999999999996
GO:0001539 T2375610003677 0.2079
GO:0001539 T2375610003678 0.2079
GO:0001539 T2375610003829 0.6082
GO:0001539 T2375610003829 0.39020000000000005
GO:0001539 T2375610003830 0.6082
GO:0001539 T2375610003830 0.39020000000000005
GO:0001539 T2375610004048 0.3333
GO:0001539 T2375610004134 0.26039999999999996
GO:0001539 T2375610004134 0.26039999999999996
GO:0001539 T2375610004137 0.26039999999999996
GO:0001539 T2375610004137 0.26039999999999996
GO:0001539 T2375610004158 0.40880000000000005
GO:0001539 T2375610004159 0.40880000000000005
GO:0001539 T2375610004192 0.7031000000000001
GO:0001539 T2375610004192 0.7031000000000001
GO:0001539 T2375610004193 0.7031000000000001
GO:0001539 T2375610004193 0.7031000000000001
GO:0001539 T2375610004233 0.36
GO:0001539 T2375610004233 0.3132
GO:0001539 T2375610004234 0.3636
GO:0001539 T2375610004234 0.2919
GO:0001539 T2375610004589 0.2775
GO:0001539 T2375610004589 0.2847
GO:0001539 T2375610004694 0.3482
GO:0001539 T2375610004694 0.3527
GO:0001539 T2375610004695 0.3482
GO:0001539 T2375610004695 0.3527
GO:0001539 T2375610004706 0.3433
GO:0001539 T2375610004706 0.33909999999999996
GO:0001539 T2375610004709 0.3433
GO:0001539 T2375610004709 0.33909999999999996
GO:0001539 T2375610004791 0.267
GO:0001539 T2375610004791 0.2673
GO:0001539 T2375610004794 0.2641
GO:0001539 T2375610004794 0.2673
GO:0001539 T2375610004804 0.36060000000000003
GO:0001539 T2375610004805 0.36060000000000003
GO:0001539 T2375610004931 0.3858
GO:0001539 T2375610004931 0.37079999999999996
GO:0001539 T2375610004932 0.3858
GO:0001539 T2375610004932 0.37079999999999996
GO:0001539 T2375610004942 0.3953
GO:0001539 T2375610004943 0.3992
GO:0001539 T2375610005058 0.5102
GO:0001539 T2375610005059 0.5102
GO:0001539 T2375610005187 0.3788
GO:0001539 T2375610005437 0.4926
GO:0001539 T2375610005438 0.4926
GO:0001539 T2375610005678 0.2671
GO:0001539 T2375610005678 0.2748
GO:0001539 T2375610005680 0.2671
GO:0001539 T2375610005680 0.2748
GO:0001539 T2375610005817 0.29100000000000004
GO:0001539 T2375610005817 0.29100000000000004
GO:0001539 T2375610005856 0.2562
GO:0001539 T2375610005857 0.2562
GO:0001539 T2375610005875 0.6595
GO:0001539 T2375610005875 0.6595
GO:0001539 T2375610006041 0.29460000000000003
GO:0001539 T2375610006077 0.2963
GO:0001539 T2375610006078 0.3009
GO:0001539 T2375610006257 0.3788
GO:0001539 T2375610006328 0.4531
GO:0001539 T2375610006328 0.4531
GO:0001539 T2375610006379 0.35710000000000003
GO:0001539 T2375610006379 0.3077
GO:0001539 T2375610006380 0.35710000000000003
GO:0001539 T2375610006380 0.3077
GO:0001539 T2375610006396 0.3772
GO:0001539 T2375610006432 0.39289999999999997
GO:0001539 T2375610006432 0.3387
GO:0001539 T2375610006790 0.3191
GO:0001539 T2375610006790 0.301
GO:0001539 T2375610006853 0.5014
GO:0001539 T2375610006853 0.5014
GO:0001539 T2375610006903 0.3086
GO:0001539 T2375610006903 0.3086
GO:0001539 T2375610006904 0.3086
GO:0001539 T2375610006904 0.3086
GO:0001539 T2375610006934 0.375
GO:0001539 T2375610007012 0.6846
GO:0001539 T2375610007012 0.33640000000000003
GO:0001539 T2375610007071 0.3689
GO:0001539 T2375610007071 0.33990000000000004
GO:0001539 T2375610007072 0.3689
GO:0001539 T2375610007072 0.33990000000000004
GO:0001539 T2375610007096 0.29710000000000003
GO:0001539 T2375610007096 0.4286
GO:0001539 T2375610007097 0.29710000000000003
GO:0001539 T2375610007097 0.4286
GO:0001539 T2375610007107 0.2887
GO:0001539 T2375610007107 0.2761
GO:0001539 T2375610007110 0.2887
GO:0001539 T2375610007110 0.2761
GO:0001539 T2375610007161 0.29460000000000003
GO:0001539 T2375610007214 0.5531
GO:0001539 T2375610007214 0.2804
GO:0001539 T2375610007215 0.5531
GO:0001539 T2375610007215 0.2804
GO:0001539 T2375610007283 0.2748
GO:0001539 T2375610007284 0.2748
GO:0001539 T2375610007332 0.5954
GO:0001539 T2375610007332 0.3757
GO:0001539 T2375610007333 0.5954
GO:0001539 T2375610007333 0.3757
GO:0001539 T2375610007391 0.47340000000000004
GO:0001539 T2375610007391 0.47340000000000004
GO:0001539 T2375610007394 0.47340000000000004
GO:0001539 T2375610007394 0.47340000000000004
GO:0001539 T2375610007466 0.33509999999999995
GO:0001539 T2375610007466 0.3299
GO:0001539 T2375610007467 0.33509999999999995
GO:0001539 T2375610007467 0.3299
GO:0001539 T2375610007595 0.3576
GO:0001539 T2375610007595 0.2891
GO:0001539 T2375610007596 0.3576
GO:0001539 T2375610007596 0.2891
GO:0001539 T2375610007661 0.45130000000000003
GO:0001539 T2375610007661 0.45130000000000003
GO:0001539 T2375610007662 0.45130000000000003
GO:0001539 T2375610007662 0.45130000000000003
GO:0001539 T2375610007712 0.4006
GO:0001539 T2375610007713 0.4006
GO:0001539 T2375610007714 0.3425
GO:0001539 T2375610007868 0.3619
GO:0001539 T2375610007868 0.3619
GO:0001539 T2375610007869 0.3619
GO:0001539 T2375610007869 0.3619
GO:0001539 T2375610007875 0.45159999999999995
GO:0001539 T2375610007876 0.45159999999999995
GO:0001539 T2375610007941 0.4982
GO:0001539 T2375610007944 0.4982
GO:0001539 T2375610007968 0.301
GO:0001539 T2375610007968 0.3131
GO:0001539 T2375610007973 0.301
GO:0001539 T2375610007973 0.3131
GO:0001539 T2375610007990 0.42
GO:0001539 T2375610007990 0.2661
GO:0001539 T2375610007991 0.42
GO:0001539 T2375610007991 0.3053
GO:0001539 T2375610008015 0.46840000000000004
GO:0001539 T2375610008182 0.3704
GO:0001539 T2375610008182 0.3691
GO:0001539 T2375610008183 0.3704
GO:0001539 T2375610008183 0.3691
GO:0001539 T2375610008234 0.4671
GO:0001539 T2375610008237 0.4671
GO:0001539 T2375610008372 0.39640000000000003
GO:0001539 T2375610008372 0.36
GO:0001539 T2375610008374 0.39640000000000003
GO:0001539 T2375610008374 0.36
GO:0001539 T2375610008445 0.2857
GO:0001539 T2375610008472 0.3547
GO:0001539 T2375610008472 0.31370000000000003
GO:0001539 T2375610008473 0.3547
GO:0001539 T2375610008473 0.31370000000000003
GO:0001539 T2375610008503 0.3095
GO:0001539 T2375610008504 0.3095
GO:0001539 T2375610008506 0.2782
GO:0001539 T2375610008506 0.2782
GO:0001539 T2375610008507 0.2782
GO:0001539 T2375610008507 0.2782
GO:0001539 T2375610008661 0.8579000000000001
GO:0001539 T2375610008693 0.6315999999999999
GO:0001539 T2375610008693 0.289
GO:0001539 T2375610008749 0.2841
GO:0001539 T2375610008749 0.26530000000000004
GO:0001539 T2375610008765 0.526
GO:0001539 T2375610008766 0.526
GO:0001539 T2375610008833 0.3425
GO:0001539 T2375610008904 0.2412
GO:0001539 T2375610008905 0.2412
GO:0001539 T2375610009052 0.2845
GO:0001539 T2375610009052 0.3875
GO:0001539 T2375610009059 0.314
GO:0001539 T2375610009059 0.29469999999999996
GO:0001539 T2375610009196 0.4696
GO:0001539 T2375610009196 0.4696
GO:0001539 T2375610009301 0.29100000000000004
GO:0001539 T2375610009301 0.29100000000000004
GO:0001539 T2375610009375 0.4407
GO:0001539 T2375610009375 0.4407
GO:0001539 T2375610009376 0.4407
GO:0001539 T2375610009376 0.4407
GO:0001539 T2375610009422 0.4386
GO:0001539 T2375610009423 0.4386
GO:0001539 T2375610009461 0.2434
GO:0001539 T2375610009462 0.2434
GO:0001539 T2375610009596 0.2186
GO:0001539 T2375610009674 0.3333
GO:0001539 T2375610009708 0.2857
GO:0001539 T2375610009721 0.3933
GO:0001539 T2375610009876 0.3125
GO:0001539 T2375610009876 0.4257
GO:0001539 T2375610009877 0.3
GO:0001539 T2375610009877 0.4257
GO:0001539 T2375610009944 0.6595
GO:0001539 T2375610009944 0.6595
GO:0001539 T2375610009960 0.4717
GO:0001539 T2375610010032 0.3811
GO:0001539 T2375610010032 0.36460000000000004
GO:0001539 T2375610010035 0.3811
GO:0001539 T2375610010035 0.36460000000000004
GO:0001539 T2375610010063 0.4717
GO:0001539 T2375610010183 0.4657
GO:0001539 T2375610010183 0.37799999999999995
GO:0001539 T2375610010186 0.4657
GO:0001539 T2375610010186 0.37799999999999995
GO:0001539 T2375610010427 0.3309
GO:0001539 T2375610010427 0.3309
GO:0001539 T2375610010428 0.3346
GO:0001539 T2375610010428 0.3346
GO:0001539 T2375610010494 0.3824
GO:0001539 T2375610010494 0.3197
GO:0001539 T2375610010501 0.3824
GO:0001539 T2375610010501 0.3197
GO:0001539 T2375610010720 0.3934
GO:0001539 T2375610010720 0.3779
GO:0001539 T2375610010721 0.3934
GO:0001539 T2375610010721 0.3779
GO:0001539 T2375610010926 0.2609
GO:0001539 T2375610010927 0.2609
GO:0001539 T2375610011107 0.314
GO:0001539 T2375610011107 0.29469999999999996
GO:0001539 T2375610011655 0.4622
GO:0001539 T2375610011655 0.4622
GO:0001539 T2375610011656 0.4622
GO:0001539 T2375610011656 0.4622
GO:0001539 T2375610011675 0.46840000000000004
GO:0001539 T2375610011687 0.4606
GO:0001539 T2375610011687 0.3243
GO:0001539 T2375610011688 0.4606
GO:0001539 T2375610011688 0.3243
GO:0001539 T2375610011690 0.3741
GO:0001539 T2375610011691 0.3741
GO:0001539 T2375610011793 0.3933
GO:0001539 T2375610011965 0.4817
GO:0001539 T2375610011968 0.4817
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In [8]:

    

import synapseclient
from synapseclient import Project, Folder, File, Link


    

In [14]:

    

syn = synapseclient.Synapse()
syn.login('yotamfra@mail.tau.ac.il', 'tsiqly12')


    

    




Welcome,  !

In [15]:

    

# project = syn.get('syn11533497') 
project = Project('CAFA_PI')
project = syn.store(project)


    

In [16]:

    

folder = Folder('submissions', parent=project)
folder = syn.store(folder)


    

In [17]:

    

data = File(osp.join(PATH, 'submission1.zip'), parent=folder)
data = syn.store(data)


    

    




##################################################
 Uploading file to Synapse storage 
##################################################

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