aboutsummaryrefslogtreecommitdiff
path: root/gn2/wqflask/do_search.py
blob: 3c81783d4b8e37a8448dd5d009815169f9eb9f71 (about) (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
import json
import re
import requests
import string

from gn2.wqflask.database import database_connection

import sys

from gn2.db import webqtlDatabaseFunction
from gn2.utility.tools import get_setting, GN2_BASE_URL


class DoSearch:
    """Parent class containing parameters/functions used for all searches"""

    # Used to translate search phrases into classes
    search_types = dict()

    def __init__(self, search_term, search_operator=None, dataset=None, search_type=None):
        self.search_term = search_term
        # Make sure search_operator is something we expect
        assert search_operator in (
            None, "=", "<", ">", "<=", ">="), "Bad search operator"
        self.search_operator = search_operator
        self.dataset = dataset
        self.search_type = search_type

        if self.dataset:
            # Get group information for dataset and the species id
            self.species_id = webqtlDatabaseFunction.retrieve_species_id(
                self.dataset.group.name)

    def execute(self, query):
        """Executes query and returns results"""
        query = self.normalize_spaces(query)
        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
            cursor.execute(query)
            return cursor.fetchall()

    def handle_wildcard(self, str):
        keyword = str.strip()
        keyword = keyword.replace("*", ".*")
        keyword = keyword.replace("?", ".")

        return keyword

    def sescape(self, item):
        """Single escape"""
        from gn2.utility.tools import get_setting
        with database_connection(get_setting("SQL_URI")) as conn:
            escaped = conn.escape_string(str(item)).decode()
        return escaped

    def mescape(self, *items):
        """Multiple escape"""
        from gn2.utility.tools import get_setting
        escaped = []
        with database_connection(get_setting("SQL_URI")) as conn:
            escaped = [conn.escape_string(str(item)).decode() for item in items]
        return tuple(escaped)

    def normalize_spaces(self, stringy):
        """Strips out newlines/extra spaces and replaces them with just spaces"""
        step_one = " ".join(stringy.split())
        return step_one

    @classmethod
    def get_search(cls, search_type):
        search_type_string = search_type['dataset_type']
        if 'key' in search_type and search_type['key'] != None:
            search_type_string += '_' + search_type['key']

        if search_type_string in cls.search_types:
            return cls.search_types[search_type_string]
        else:
            return None


class MrnaAssaySearch(DoSearch):
    """A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites"""

    DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch"

    base_query = """
                SELECT DISTINCT
                ProbeSetFreeze.`Name`,
                ProbeSetFreeze.`FullName`,
                ProbeSet.`Name`,
                ProbeSet.`Symbol`,
                CAST(ProbeSet.`description` AS BINARY),
                CAST(ProbeSet.`Probe_Target_Description` AS BINARY),
                ProbeSet.`Chr`,
                ProbeSet.`Mb`,
                ProbeSetXRef.`Mean`,
                ProbeSetXRef.`LRS`,
                ProbeSetXRef.`Locus`,
                ProbeSetXRef.`pValue`,
                ProbeSetXRef.`additive`,
                Geno.`Chr` as geno_chr,
                Geno.`Mb` as geno_mb
                FROM Species
                INNER JOIN InbredSet ON InbredSet.`SpeciesId`= Species.`Id`
                INNER JOIN ProbeFreeze ON ProbeFreeze.`InbredSetId` = InbredSet.`Id`
                INNER JOIN Tissue ON ProbeFreeze.`TissueId` = Tissue.`Id`
                INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.`ProbeFreezeId` = ProbeFreeze.`Id`
                INNER JOIN ProbeSetXRef ON ProbeSetXRef.`ProbeSetFreezeId` = ProbeSetFreeze.`Id`
                INNER JOIN ProbeSet ON ProbeSet.`Id` = ProbeSetXRef.`ProbeSetId`
                LEFT JOIN Geno ON ProbeSetXRef.`Locus` = Geno.`Name` AND Geno.`SpeciesId` = Species.`Id` """

    header_fields = ['Index',
                     'Record',
                     'Symbol',
                     'Description',
                     'Location',
                     'Mean',
                     'Max LRS',
                     'Max LRS Location',
                     'Additive Effect']

    def get_alias_where_clause(self):
        search_string = self.sescape(self.search_term[0])

        if self.search_term[0] != "*":
            match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % (
                search_string)
        else:
            match_clause = ""

        where_clause = (match_clause
                        + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
               and ProbeSetXRef.ProbeSetFreezeId = %s
                        """ % (self.sescape(str(self.dataset.id))))

        return where_clause

    def get_where_clause(self):
        search_string = self.sescape(self.search_term[0])

        if self.search_term[0] != "*":
            if re.search("\w{1,2}\-\w+|\w+\-\w{1,2}", self.search_term[0]):
                search_string = f'"{search_string}*"'

            match_clause = f"""((MATCH (ProbeSet.Name,
                        ProbeSet.description,
                        ProbeSet.symbol,
                        alias,
                        GenbankId,
                        UniGeneId,
                        Probe_Target_Description)
                        AGAINST ('{search_string}' IN BOOLEAN MODE))) AND """
        else:
            match_clause = ""

        where_clause = (match_clause
                        + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
               and ProbeSetXRef.ProbeSetFreezeId = %s
                        """ % (self.sescape(str(self.dataset.id))))

        return where_clause

    def compile_final_query(self, from_clause='', where_clause=''):
        """Generates the final query string"""

        from_clause = self.normalize_spaces(from_clause)

        query = (self.base_query +
                 """%s
                WHERE %s
                    and ProbeSet.Id = ProbeSetXRef.ProbeSetId
                    and ProbeSetXRef.ProbeSetFreezeId = %s
                ORDER BY ProbeSet.symbol ASC
                            """ % (self.sescape(from_clause),
                                   where_clause,
                                   self.sescape(str(self.dataset.id))))
        return query

    def run_combined(self, from_clause='', where_clause=''):
        """Generates and runs a combined search of an mRNA expression dataset"""
        #query = self.base_query + from_clause + " WHERE " + where_clause

        from_clause = self.normalize_spaces(from_clause)

        query = (self.base_query +
                 """%s
                WHERE %s
                    and ProbeSet.Id = ProbeSetXRef.ProbeSetId
                    and ProbeSetXRef.ProbeSetFreezeId = %s
                ORDER BY ProbeSet.symbol ASC
                            """ % (self.sescape(from_clause),
                                   where_clause,
                                   self.sescape(str(self.dataset.id))))

        return self.execute(query)

    def run(self):
        """Generates and runs a simple search of an mRNA expression dataset"""
        where_clause = self.get_where_clause()
        query = self.base_query + "WHERE " + where_clause + "ORDER BY ProbeSet.symbol ASC"
        return self.execute(query)


class PhenotypeSearch(DoSearch):
    """A search within a phenotype dataset"""

    DoSearch.search_types['Publish'] = "PhenotypeSearch"

    base_query = """SELECT PublishXRef.Id,
                CAST(Phenotype.`Pre_publication_description` AS BINARY),
                CAST(Phenotype.`Post_publication_description` AS BINARY),
                Publication.`Authors`,
                Publication.`Year`,
                Publication.`PubMed_ID`,
                PublishXRef.`mean`,
                PublishXRef.`LRS`,
                PublishXRef.`additive`,
                PublishXRef.`Locus`,
                InbredSet.`InbredSetCode`,
                Geno.`Chr`,
                Geno.`Mb`
                FROM Species
                INNER JOIN InbredSet ON InbredSet.`SpeciesId` = Species.`Id`
                INNER JOIN PublishXRef ON PublishXRef.`InbredSetId` = InbredSet.`Id`
                INNER JOIN PublishFreeze ON PublishFreeze.`InbredSetId` = InbredSet.`Id`
                INNER JOIN Publication ON Publication.`Id` = PublishXRef.`PublicationId`
                INNER JOIN Phenotype ON Phenotype.`Id` = PublishXRef.`PhenotypeId`
                LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id """

    search_fields = ('Phenotype.Post_publication_description',
                     'Phenotype.Pre_publication_description',
                     'Phenotype.Pre_publication_abbreviation',
                     'Phenotype.Post_publication_abbreviation',
                     'Phenotype.Lab_code',
                     'Publication.PubMed_ID',
                     'Publication.Abstract',
                     'Publication.Title',
                     'Publication.Authors',
                     'PublishXRef.Id')

    header_fields = ['Index',
                     'Record',
                     'Description',
                     'Mean',
                     'Authors',
                     'Year',
                     'Max LRS',
                     'Max LRS Location',
                     'Additive Effect']

    def get_where_clause(self):
        """Generate clause for WHERE portion of query"""

        # Todo: Zach will figure out exactly what both these lines mean
        # and comment here

        # if "'" not in self.search_term[0]:
        search_term = "%" + \
            self.handle_wildcard(self.search_term[0]) + "%"
        if "_" in self.search_term[0]:
            if len(self.search_term[0].split("_")[0]) == 3:
                search_term = "%" + self.handle_wildcard(
                    self.search_term[0].split("_")[1]) + "%"

        # This adds a clause to the query that matches the search term
        # against each field in the search_fields tuple
        where_clause_list = []
        for field in self.search_fields:
            where_clause_list.append('''%s LIKE "%s"''' %
                                     (field, search_term))
        where_clause = "(%s) " % ' OR '.join(where_clause_list)

        return where_clause

    def compile_final_query(self, from_clause='', where_clause=''):
        """Generates the final query string"""

        from_clause = self.normalize_spaces(from_clause)

        if self.search_term[0] == "*":
            query = (self.base_query +
                     """%s
                        WHERE PublishXRef.InbredSetId = %s
                        and PublishXRef.PhenotypeId = Phenotype.Id
                        and PublishXRef.PublicationId = Publication.Id
                        and PublishFreeze.Id = %s
                        ORDER BY PublishXRef.Id""" % (
                         from_clause,
                         self.sescape(str(self.dataset.group.id)),
                         self.sescape(str(self.dataset.id))))
        else:
            query = (self.base_query +
                     """%s
                        WHERE %s
                        and PublishXRef.InbredSetId = %s
                        and PublishXRef.PhenotypeId = Phenotype.Id
                        and PublishXRef.PublicationId = Publication.Id
                        and PublishFreeze.Id = %s
                        ORDER BY PublishXRef.Id""" % (
                         from_clause,
                         where_clause,
                         self.sescape(str(self.dataset.group.id)),
                         self.sescape(str(self.dataset.id))))

        return query

    def run_combined(self, from_clause, where_clause):
        """Generates and runs a combined search of an phenotype dataset"""
        from_clause = self.normalize_spaces(from_clause)

        query = (self.base_query +
                 """%s
                    WHERE %s
                    PublishXRef.InbredSetId = %s and
                    PublishXRef.PhenotypeId = Phenotype.Id and
                    PublishXRef.PublicationId = Publication.Id and
                    PublishFreeze.Id = %s""" % (
                     from_clause,
                     where_clause,
                     self.sescape(str(self.dataset.group.id)),
                     self.sescape(str(self.dataset.id))))

        return self.execute(query)

    def run(self):
        """Generates and runs a simple search of a phenotype dataset"""

        query = self.compile_final_query(where_clause=self.get_where_clause())

        return self.execute(query)


class GenotypeSearch(DoSearch):
    """A search within a genotype dataset"""

    DoSearch.search_types['Geno'] = "GenotypeSearch"

    base_query = """SELECT Geno.Name,
                GenoFreeze.createtime as thistable,
                Geno.Name as Geno_Name,
                Geno.Source2 as Geno_Source2,
                Geno.Chr as Geno_Chr,
                Geno.Mb as Geno_Mb
                FROM GenoXRef, GenoFreeze, Geno """

    search_fields = ('Name', 'Chr')

    header_fields = ['Index',
                     'Record',
                     'Location']

    def get_where_clause(self):
        """Generate clause for part of the WHERE portion of query"""

        # This adds a clause to the query that matches the search term
        # against each field in search_fields (above)
        where_clause = []

        if "'" not in self.search_term[0]:
            self.search_term = "%" + self.search_term[0] + "%"

        for field in self.search_fields:
            where_clause.append('''%s LIKE "%s"''' % ("%s.%s" % self.mescape(self.dataset.type,
                                                                               field),
                                                        self.search_term))
        where_clause = "(%s) " % ' OR '.join(where_clause)

        return where_clause

    def compile_final_query(self, from_clause='', where_clause=''):
        """Generates the final query string"""

        from_clause = self.normalize_spaces(from_clause)

        if self.search_term[0] == "*":
            query = (self.base_query
                     + """WHERE Geno.Id = GenoXRef.GenoId
                        and GenoXRef.GenoFreezeId = GenoFreeze.Id
                        and GenoFreeze.Id = %s""" % (self.sescape(str(self.dataset.id))))
        else:
            query = (self.base_query +
                     """WHERE %s
                        and Geno.Id = GenoXRef.GenoId
                        and GenoXRef.GenoFreezeId = GenoFreeze.Id
                        and GenoFreeze.Id = %s""" % (where_clause,
                                                     self.sescape(str(self.dataset.id))))

        return query

    def run(self):
        """Generates and runs a simple search of a genotype dataset"""
        # Todo: Zach will figure out exactly what both these lines mean
        # and comment here

        if self.search_term[0] == "*":
            self.query = self.compile_final_query()
        else:
            self.query = self.compile_final_query(
                where_clause=self.get_where_clause())

        return self.execute(self.query)


class RifSearch(MrnaAssaySearch):
    """Searches for traits with a Gene RIF entry including the search term."""

    DoSearch.search_types['ProbeSet_RIF'] = "RifSearch"

    def get_from_clause(self):
        return f" INNER JOIN GeneRIF_BASIC ON GeneRIF_BASIC.`symbol` = { self.dataset.type }.`symbol` "

    def get_where_clause(self):
        where_clause = f"(MATCH (GeneRIF_BASIC.comment) AGAINST ('+{ self.search_term[0] }' IN BOOLEAN MODE)) "

        return where_clause

    def run(self):
        from_clause = self.get_from_clause()
        where_clause = self.get_where_clause()

        query = self.compile_final_query(from_clause, where_clause)

        return self.execute(query)


class WikiSearch(MrnaAssaySearch):
    """Searches GeneWiki for traits other people have annotated"""

    DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch"

    def get_from_clause(self):
        return ", GeneRIF "

    def get_where_clause(self):
        where_clause = """%s.symbol = GeneRIF.symbol
            and GeneRIF.versionId=0 and GeneRIF.display>0
            and (GeneRIF.comment LIKE '%s' or GeneRIF.initial = '%s')
                """ % (self.dataset.type,
                       "%" + str(self.search_term[0]) + "%",
                       str(self.search_term[0]))
        return where_clause

    def run(self):
        from_clause = self.get_from_clause()
        where_clause = self.get_where_clause()

        query = self.compile_final_query(from_clause, where_clause)

        return self.execute(query)


class GoSearch(MrnaAssaySearch):
    """Searches for synapse-associated genes listed in the Gene Ontology."""

    DoSearch.search_types['ProbeSet_GO'] = "GoSearch"

    def get_from_clause(self):
        from_clause = """, db_GeneOntology.term as GOterm,
            db_GeneOntology.association as GOassociation,
            db_GeneOntology.gene_product as GOgene_product """

        return from_clause

    def get_where_clause(self):
        field = 'GOterm.acc'
        go_id = 'GO:' + ('0000000' + self.search_term[0])[-7:]

        statements = ("""%s.symbol=GOgene_product.symbol and
           GOassociation.gene_product_id=GOgene_product.id and
           GOterm.id=GOassociation.term_id""" % (
            self.sescape(self.dataset.type)))

        where_clause = " %s = '%s' and %s " % (field, go_id, statements)

        return where_clause

    def run(self):
        from_clause = self.get_from_clause()
        where_clause = self.get_where_clause()

        query = self.compile_final_query(from_clause, where_clause)

        return self.execute(query)

# ZS: Not sure what the best way to deal with LRS searches is


class LrsSearch(DoSearch):
    """Searches for genes with a QTL within the given LRS values

    LRS searches can take 3 different forms:
    - LRS > (or <) min/max_LRS
    - LRS=(min_LRS max_LRS)
    - LRS=(min_LRS max_LRS chromosome start_Mb end_Mb)
    where min/max_LRS represent the range of LRS scores and start/end_Mb represent
    the range in megabases on the given chromosome

    """

    for search_key in ('LRS', 'LOD'):
        DoSearch.search_types[search_key] = "LrsSearch"

    def get_from_clause(self):
        converted_search_term = []
        for value in self.search_term:
            try:
                converted_search_term.append(float(value))
            except:
                converted_search_term.append(value)

        self.search_term = converted_search_term

        from_clause = ""

        return from_clause

    def get_where_clause(self):
        if self.search_operator == "=":
            assert isinstance(self.search_term, (list, tuple))
            lrs_min, lrs_max = self.search_term[:2]
            if self.search_type == "LOD":
                lrs_min = lrs_min * 4.61
                lrs_max = lrs_max * 4.61

            where_clause = """ %sXRef.LRS > %s and
                             %sXRef.LRS < %s """ % self.mescape(self.dataset.type,
                                                                min(lrs_min,
                                                                    lrs_max),
                                                                self.dataset.type,
                                                                max(lrs_min, lrs_max))

            if len(self.search_term) > 2:
                try:
                    chr_num = int(float(self.search_term[2]))
                except:
                    chr_num = self.search_term[2].lower().replace('chr', '')
                self.search_term[2] = chr_num

                where_clause += """ and Geno.Chr = '%s' """ % (chr_num)
                if len(self.search_term) == 5:
                    mb_low, mb_high = self.search_term[3:]
                    where_clause += """ and Geno.Mb > %s and
                                                  Geno.Mb < %s
                                            """ % self.mescape(min(mb_low, mb_high),
                                                               max(mb_low, mb_high))

                where_clause += """ and %sXRef.Locus = Geno.name and
                                                    Geno.SpeciesId = %s
                                                    """ % self.mescape(self.dataset.type,
                                                                       self.species_id)
        else:
            # Deal with >, <, >=, and <=
            lrs_val = self.search_term[0]
            if self.search_type == "LOD":
                lrs_val = lrs_val * 4.61

            where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type,
                                                                   self.search_operator,
                                                                   self.search_term[0])

        return where_clause

    def run(self):

        self.from_clause = self.get_from_clause()
        self.where_clause = self.get_where_clause()

        self.query = self.compile_final_query(
            self.from_clause, self.where_clause)

        return self.execute(self.query)


class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):

    for search_key in ('LRS', 'LOD'):
        DoSearch.search_types['ProbeSet_' + search_key] = "MrnaLrsSearch"

    def run(self):
        self.from_clause = self.get_from_clause()
        self.where_clause = self.get_where_clause()

        self.query = self.compile_final_query(
            from_clause=self.from_clause, where_clause=self.where_clause)

        return self.execute(self.query)


class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):

    for search_key in ('LRS', 'LOD'):
        DoSearch.search_types['Publish_' + search_key] = "PhenotypeLrsSearch"

    def run(self):

        self.from_clause = self.get_from_clause()
        self.where_clause = self.get_where_clause()

        self.query = self.compile_final_query(
            from_clause=self.from_clause, where_clause=self.where_clause)

        return self.execute(self.query)


class CisTransLrsSearch(DoSearch):

    def get_where_clause(self, cis_trans):
        self.mb_buffer = 5  # default
        chromosome = None
        if cis_trans == "cis":
            the_operator = "<"
        else:
            the_operator = ">"

        if self.search_operator == "=":
            if len(self.search_term) == 2 or len(self.search_term) == 3:
                self.search_term = [float(value) for value in self.search_term]
            if len(self.search_term) == 2:
                lrs_min, lrs_max = self.search_term
                #[int(value) for value in self.search_term]
            elif len(self.search_term) == 3:
                lrs_min, lrs_max, self.mb_buffer = self.search_term
            elif len(self.search_term) == 4:
                lrs_min, lrs_max, self.mb_buffer = [
                    float(value) for value in self.search_term[:3]]
                chromosome = self.search_term[3]
                chr_str = re.match("(^c|^C)[a-z]*", chromosome)
                if chr_str:
                    chromosome = int(chromosome.replace(chr_str.group(0), ''))
            else:
                SomeError

            if self.search_type == "CISLOD" or self.search_type == "TRANSLOD":
                lrs_min = lrs_min * 4.61
                lrs_max = lrs_max * 4.61

            sub_clause = """ %sXRef.LRS > %s and
                %sXRef.LRS < %s  and """ % (
                self.sescape(self.dataset.type),
                self.sescape(str(min(lrs_min, lrs_max))),
                self.sescape(self.dataset.type),
                self.sescape(str(max(lrs_min, lrs_max)))
            )
        else:
            # Deal with >, <, >=, and <=
            sub_clause = """ %sXRef.LRS %s %s and """ % (
                self.sescape(self.dataset.type),
                self.sescape(self.search_operator),
                self.sescape(self.search_term[0])
            )

        if cis_trans == "cis":
            where_clause = sub_clause + """
                    ABS(%s.Mb-Geno.Mb) %s %s and
                    %sXRef.Locus = Geno.name and
                    Geno.SpeciesId = %s and
                    %s.Chr = Geno.Chr""" % (
                self.sescape(self.dataset.type),
                the_operator,
                self.sescape(str(self.mb_buffer)),
                self.sescape(self.dataset.type),
                self.sescape(str(self.species_id)),
                self.sescape(self.dataset.type)
            )
        else:
            if chromosome:
                location_clause = """
                        (%s.Chr = '%s' and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) 
                        or (%s.Chr != Geno.Chr and Geno.Chr = '%s')""" % (
                    self.sescape(self.dataset.type),
                    chromosome,
                    self.sescape(
                    self.dataset.type),
                    self.sescape(
                    self.dataset.type),
                    the_operator,
                    self.sescape(
                    str(self.mb_buffer)),
                    self.sescape(
                    self.dataset.type),
                    chromosome)
            else:
                location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (self.sescape(
                    self.dataset.type), the_operator, self.sescape(str(self.mb_buffer)), self.sescape(self.dataset.type), self.sescape(self.dataset.type))
            where_clause = sub_clause + """
                    %sXRef.Locus = Geno.name and
                    Geno.SpeciesId = %s and
                    (%s)""" % (
                self.sescape(self.dataset.type),
                self.sescape(str(self.species_id)),
                location_clause
            )

        return where_clause


class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
    """
    Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values

    A cisLRS search can take 3 forms:
    - cisLRS=(min_LRS max_LRS)
    - cisLRS=(min_LRS max_LRS mb_buffer)
    - cisLRS>min_LRS
    where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around
    a particular QTL where its eQTL would be considered "cis". If there is no third parameter,
    mb_buffer will default to 5 megabases.

    A QTL is a cis-eQTL if a gene's expression is regulated by a QTL in roughly the same area
    (where the area is determined by the mb_buffer that the user can choose).

    """

    for search_key in ('LRS', 'LOD'):
        DoSearch.search_types['ProbeSet_CIS' + search_key] = "CisLrsSearch"

    def get_where_clause(self):
        return CisTransLrsSearch.get_where_clause(self, "cis")

    def run(self):
        self.from_clause = self.get_from_clause()
        self.where_clause = self.get_where_clause()

        self.query = self.compile_final_query(
            self.from_clause, self.where_clause)

        return self.execute(self.query)


class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
    """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values

    A transLRS search can take 3 forms:
    - transLRS=(min_LRS max_LRS)
    - transLRS=(min_LRS max_LRS mb_buffer)
    - transLRS>min_LRS
    where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around
    a particular QTL where its eQTL would be considered "cis". If there is no third parameter,
    mb_buffer will default to 5 megabases.

    A QTL is a trans-eQTL if a gene's expression is regulated by a QTL in a different location/area
    (where the area is determined by the mb_buffer that the user can choose). Opposite of cis-eQTL.

    """

    for search_key in ('LRS', 'LOD'):
        DoSearch.search_types['ProbeSet_TRANS' + search_key] = "TransLrsSearch"

    def get_where_clause(self):
        return CisTransLrsSearch.get_where_clause(self, "trans")

    def run(self):
        self.from_clause = self.get_from_clause()
        self.where_clause = self.get_where_clause()

        self.query = self.compile_final_query(
            self.from_clause, self.where_clause)

        return self.execute(self.query)


class MeanSearch(MrnaAssaySearch):
    """Searches for genes expressed within an interval (log2 units) determined by the user"""

    DoSearch.search_types['ProbeSet_MEAN'] = "MeanSearch"

    def get_where_clause(self):
        self.search_term = [float(value) for value in self.search_term]

        if self.search_operator == "=":
            assert isinstance(self.search_term, (list, tuple))
            self.mean_min, self.mean_max = self.search_term[:2]

            where_clause = """ %sXRef.mean > %s and
                             %sXRef.mean < %s """ % self.mescape(self.dataset.type,
                                                                 min(self.mean_min,
                                                                     self.mean_max),
                                                                 self.dataset.type,
                                                                 max(self.mean_min, self.mean_max))
        else:
            # Deal with >, <, >=, and <=
            where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type,
                                                                    self.search_operator,
                                                                    self.search_term[0])

        return where_clause

    def run(self):
        self.where_clause = self.get_where_clause()

        self.query = self.compile_final_query(where_clause=self.where_clause)

        return self.execute(self.query)


class RangeSearch(MrnaAssaySearch):
    """Searches for genes with a range of expression varying between two values"""

    DoSearch.search_types['ProbeSet_RANGE'] = "RangeSearch"

    def get_where_clause(self):
        if self.search_operator == "=":
            assert isinstance(self.search_term, (list, tuple))
            self.range_min, self.range_max = self.search_term[:2]
            where_clause = """ (SELECT Pow(2, max(value) -min(value))
                                     FROM ProbeSetData
                                     WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND
                                    (SELECT Pow(2, max(value) -min(value))
                                     FROM ProbeSetData
                                     WHERE ProbeSetData.Id = ProbeSetXRef.dataId) < %s
                                    """ % self.mescape(min(self.range_min, self.range_max),
                                                       max(self.range_min, self.range_max))
        else:
            # Deal with >, <, >=, and <=
            where_clause = """ (SELECT Pow(2, max(value) -min(value))
                                     FROM ProbeSetData
                                     WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s
                                    """ % (self.sescape(self.search_term[0]))
        return where_clause

    def run(self):
        self.where_clause = self.get_where_clause()

        self.query = self.compile_final_query(where_clause=self.where_clause)

        return self.execute(self.query)


class PositionSearch(DoSearch):
    """Searches for genes/markers located within a specified range on a specified chromosome"""

    for search_key in ('POSITION', 'POS', 'MB'):
        DoSearch.search_types[search_key] = "PositionSearch"

    def get_where_clause(self):
        self.search_term = [float(value) if is_number(
            value) else value for value in self.search_term]
        chr, self.mb_min, self.mb_max = self.search_term[:3]
        self.chr = str(chr).lower()
        self.get_chr()

        where_clause = """ %s.Chr = '%s' and
                                %s.Mb > %s and
                                %s.Mb < %s """ % self.mescape(self.dataset.type,
                                                              self.chr,
                                                              self.dataset.type,
                                                              min(self.mb_min,
                                                                  self.mb_max),
                                                              self.dataset.type,
                                                              max(self.mb_min, self.mb_max))

        return where_clause

    def get_chr(self):
        try:
            self.chr = int(float(self.chr))
        except:
            self.chr = self.chr.lower().replace('chr', '')

    def run(self):

        self.get_where_clause()
        self.query = self.compile_final_query(where_clause=self.where_clause)

        return self.execute(self.query)


class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
    """Searches for genes located within a specified range on a specified chromosome"""

    for search_key in ('POSITION', 'POS', 'MB'):
        DoSearch.search_types['ProbeSet_' + search_key] = "MrnaPositionSearch"

    def run(self):

        self.where_clause = self.get_where_clause()
        self.query = self.compile_final_query(where_clause=self.where_clause)

        return self.execute(self.query)


class GenotypePositionSearch(PositionSearch, GenotypeSearch):
    """Searches for genes located within a specified range on a specified chromosome"""

    for search_key in ('POSITION', 'POS', 'MB'):
        DoSearch.search_types['Geno_' + search_key] = "GenotypePositionSearch"

    def run(self):

        self.where_clause = self.get_where_clause()
        self.query = self.compile_final_query(where_clause=self.where_clause)

        return self.execute(self.query)


class PvalueSearch(MrnaAssaySearch):
    """Searches for traits with a permutationed p-value between low and high"""

    DoSearch.search_types['ProbeSet_PVALUE'] = "PvalueSearch"

    def run(self):

        self.search_term = [float(value) for value in self.search_term]

        if self.search_operator == "=":
            assert isinstance(self.search_term, (list, tuple))
            self.pvalue_min, self.pvalue_max = self.search_term[:2]
            self.where_clause = """ %sXRef.pValue > %s and %sXRef.pValue < %s
                                    """ % self.mescape(
                self.dataset.type,
                min(self.pvalue_min, self.pvalue_max),
                self.dataset.type,
                max(self.pvalue_min, self.pvalue_max))
        else:
            # Deal with >, <, >=, and <=
            self.where_clause = """ %sXRef.pValue %s %s
                                    """ % self.mescape(
                self.dataset.type,
                self.search_operator,
                self.search_term[0])

        self.query = self.compile_final_query(where_clause=self.where_clause)
        return self.execute(self.query)


class AuthorSearch(PhenotypeSearch):
    """Searches for phenotype traits with specified author(s)"""

    DoSearch.search_types["Publish_NAME"] = "AuthorSearch"

    def run(self):
        search_term = "%" + self.search_term[0] + "%"
        self.where_clause = """ Publication.Authors LIKE "%s" and
                                """ % (search_term)

        self.query = self.compile_final_query(where_clause=self.where_clause)

        return self.execute(self.query)


def is_number(s):
    try:
        float(s)
        return True
    except ValueError:
        return False


if __name__ == "__main__":
    # Usually this will be used as a library, but call it from the command line for testing
    # And it runs the code below
    import sys

    from gn2.base import webqtlConfig
    from gn2.base.data_set import create_dataset
    from gn2.utility import webqtlUtil
    from gn2.db import webqtlDatabaseFunction

    from gn2.wqflask.database import database_connection

    with database_connection(get_setting("SQL_URI")) as db_conn:
        with db_conn.cursor() as cursor:
            dataset_name = "HC_M2_0606_P"
            dataset = create_dataset(db_conn, dataset_name)

            results = PvalueSearch(['0.005'], '<', dataset, cursor, db_conn).run()