aboutsummaryrefslogtreecommitdiff
path: root/wqflask/base/trait.py
blob: 5903fb08d1ced94a3d5ec439c48d234139588cba (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
from __future__ import absolute_import, division, print_function

import os
import string
import resource
import codecs
import requests
import random
import urllib

from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
from base.data_set import create_dataset
from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility import hmac
from utility.authentication_tools import check_resource_availability
from utility.tools import GN2_BASE_URL, GN_VERSION
from utility.redis_tools import get_redis_conn, get_resource_id, get_resource_info
Redis = get_redis_conn()

from wqflask import app

import simplejson as json
from MySQLdb import escape_string as escape
from pprint import pformat as pf

from flask import Flask, g, request, url_for, redirect, make_response, render_template

from utility.logger import getLogger
logger = getLogger(__name__ )

def create_trait(**kw):
    assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";

    permitted = True
    if kw.get('name'):
        if kw.get('dataset_name'):
            if kw.get('dataset_name') != "Temp":
                dataset = create_dataset(kw.get('dataset_name'))
        else:
            dataset = kw.get('dataset')

        if kw.get('dataset_name') != "Temp":
            if dataset.type == 'Publish':
                permissions = check_resource_availability(dataset, kw.get('name'))
            else:
                permissions = check_resource_availability(dataset)

    if "view" in permissions['data']:
        the_trait = GeneralTrait(**kw)
        if the_trait.dataset.type != "Temp":

            the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
        return the_trait
    else:
        return None

class GeneralTrait(object):
    """
    Trait class defines a trait in webqtl, can be either Microarray,
    Published phenotype, genotype, or user input trait

    """

    def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
        # xor assertion
        assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
        self.name = kw.get('name')                 # Trait ID, ProbeSet ID, Published ID, etc.
        if kw.get('dataset_name'):
            if kw.get('dataset_name') == "Temp":
                temp_group = self.name.split("_")[2]
                self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
            else:
                self.dataset = create_dataset(kw.get('dataset_name'))
        else:
            self.dataset = kw.get('dataset')
        self.cellid = kw.get('cellid')
        self.identification = kw.get('identification', 'un-named trait')
        self.haveinfo = kw.get('haveinfo', False)
        self.sequence = kw.get('sequence')         # Blat sequence, available for ProbeSet
        self.data = kw.get('data', {})
        self.view = True

        # Sets defaults
        self.locus = None
        self.lrs = None
        self.pvalue = None
        self.mean = None
        self.additive = None
        self.num_overlap = None
        self.strand_probe = None
        self.symbol = None
        self.display_name = self.name

        self.LRS_score_repr = "N/A"
        self.LRS_location_repr = "N/A"

        if kw.get('fullname'):
            name2 = value.split("::")
            if len(name2) == 2:
                self.dataset, self.name = name2
                # self.cellid is set to None above
            elif len(name2) == 3:
                self.dataset, self.name, self.cellid = name2

        # Todo: These two lines are necessary most of the time, but perhaps not all of the time
        # So we could add a simple if statement to short-circuit this if necessary
        if get_sample_info != False:
            self = retrieve_sample_data(self, self.dataset)

    def export_informative(self, include_variance=0):
        """
        export informative sample
        mostly used in qtl regression

        """
        samples = []
        vals = []
        the_vars = []
        sample_aliases = []
        for sample_name, sample_data in self.data.items():
            if sample_data.value != None:
                if not include_variance or sample_data.variance != None:
                    samples.append(sample_name)
                    vals.append(sample_data.value)
                    the_vars.append(sample_data.variance)
                    sample_aliases.append(sample_data.name2)
        return  samples, vals, the_vars, sample_aliases

    @property
    def description_fmt(self):
        '''Return a text formated description'''
        if self.dataset.type == 'ProbeSet':
            if self.description:
                formatted = self.description
                if self.probe_target_description:
                    formatted += "; " + self.probe_target_description
            else:
                formatted = "Not available"
        elif self.dataset.type == 'Publish':
            if self.confidential:
                formatted = self.pre_publication_description
            else:
                formatted = self.post_publication_description
        else:
            formatted = "Not available"

        return formatted

    @property
    def alias_fmt(self):
        '''Return a text formatted alias'''

        alias = 'Not available'
        if self.alias:
            alias = string.replace(self.alias, ";", " ")
            alias = string.join(string.split(alias), ", ")

        return alias

    @property
    def wikidata_alias_fmt(self):
        '''Return a text formatted alias'''

        alias = 'Not available'
        if self.symbol:
            human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
            mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
            other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())

            if human_response and mouse_response and other_response:
                alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content)

                filtered_aliases = []
                seen = set()
                for item in alias_list:
                    if item in seen:
                        continue
                    else:
                        filtered_aliases.append(item)
                        seen.add(item)
                alias = "; ".join(filtered_aliases)

        return alias


    @property
    def location_fmt(self):
        '''Return a text formatted location

        While we're at it we set self.location in case we need it later (do we?)

        '''

        if self.chr and self.mb:
            self.location = 'Chr %s @ %s Mb'  % (self.chr,self.mb)
        elif self.chr:
            self.location = 'Chr %s @ Unknown position' % (self.chr)
        else:
            self.location = 'Not available'

        fmt = self.location
        ##XZ: deal with direction
        if self.strand_probe == '+':
            fmt += (' on the plus strand ')
        elif self.strand_probe == '-':
            fmt += (' on the minus strand ')

        return fmt
        
def retrieve_sample_data(trait, dataset, samplelist=None):
    if samplelist == None:
        samplelist = []

    if dataset.type == "Temp":
        results = Redis.get(trait.name).split()
    else:
        results = dataset.retrieve_sample_data(trait.name)

    # Todo: is this necessary? If not remove
    trait.data.clear()

    if results:
        if dataset.type == "Temp":
            all_samples_ordered = dataset.group.all_samples_ordered()
            for i, item in enumerate(results):
                try:
                    trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
                except:
                    pass
        else:
            for item in results:
                name, value, variance, num_cases, name2 = item
                if not samplelist or (samplelist and name in samplelist):
                    trait.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
    return trait

@app.route("/trait/get_sample_data")
def get_sample_data():
    params = request.args
    trait = params['trait']
    dataset = params['dataset']

    trait_ob = create_trait(name=trait, dataset_name=dataset)
    if trait_ob:
        trait_dict = {}
        trait_dict['name'] = trait
        trait_dict['db'] = dataset
        trait_dict['type'] = trait_ob.dataset.type
        trait_dict['group'] = trait_ob.dataset.group.name
        trait_dict['tissue'] = trait_ob.dataset.tissue
        trait_dict['species'] = trait_ob.dataset.group.species
        trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
        trait_dict['description'] = trait_ob.description_display
        if trait_ob.dataset.type == "ProbeSet":
            trait_dict['symbol'] = trait_ob.symbol
            trait_dict['location'] = trait_ob.location_repr
        elif trait_ob.dataset.type == "Publish":
            if trait_ob.pubmed_id:
                trait_dict['pubmed_link'] = trait_ob.pubmed_link
            trait_dict['pubmed_text'] = trait_ob.pubmed_text

        return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
    else:
        return None
    
def jsonable(trait):
    """Return a dict suitable for using as json

    Actual turning into json doesn't happen here though"""

    dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
    
    if dataset.type == "ProbeSet":
        return dict(name=trait.name,
                    symbol=trait.symbol,
                    dataset=dataset.name,
                    dataset_name = dataset.shortname,
                    description=trait.description_display,
                    mean=trait.mean,
                    location=trait.location_repr,
                    lrs_score=trait.LRS_score_repr,
                    lrs_location=trait.LRS_location_repr,
                    additive=trait.additive
                    )
    elif dataset.type == "Publish":
        if trait.pubmed_id:
            return dict(name=trait.name,
                        dataset=dataset.name,
                        dataset_name = dataset.shortname,
                        description=trait.description_display,
                        abbreviation=trait.abbreviation,
                        authors=trait.authors,
                        pubmed_text=trait.pubmed_text,
                        pubmed_link=trait.pubmed_link,
                        lrs_score=trait.LRS_score_repr,
                        lrs_location=trait.LRS_location_repr,
                        additive=trait.additive
                        )
        else:
            return dict(name=trait.name,
                        dataset=dataset.name,
                        dataset_name = dataset.shortname,
                        description=trait.description_display,
                        abbreviation=trait.abbreviation,
                        authors=trait.authors,
                        pubmed_text=trait.pubmed_text,
                        lrs_score=trait.LRS_score_repr,
                        lrs_location=trait.LRS_location_repr,
                        additive=trait.additive
                        )
    elif dataset.type == "Geno":
        return dict(name=trait.name,
                    dataset=dataset.name,
                    dataset_name = dataset.shortname,
                    location=trait.location_repr
                    )
    else:
        return dict()

def jsonable_table_row(trait, dataset_name, index):
    """Return a list suitable for json and intended to be displayed in a table

    Actual turning into json doesn't happen here though"""

    dataset = create_dataset(dataset_name)
    
    if dataset.type == "ProbeSet":
        if trait.mean == "":
            mean = "N/A"
        else:
            mean = "%.3f" % round(float(trait.mean), 2)
        if trait.additive == "":
            additive = "N/A"
        else:
            additive = "%.3f" % round(float(trait.additive), 2)
        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                index,
                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
                trait.symbol,
                trait.description_display,
                trait.location_repr,
                mean, 
                trait.LRS_score_repr,
                trait.LRS_location_repr,
                additive]
    elif dataset.type == "Publish":
        if trait.additive == "":
            additive = "N/A"
        else:
            additive = "%.2f" % round(float(trait.additive), 2)
        if trait.pubmed_id:
            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                    index,
                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
                    trait.description_display,
                    trait.authors,
                    '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>',
                    trait.LRS_score_repr,
                    trait.LRS_location_repr,
                    additive]
        else:
            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                    index,
                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
                    trait.description_display,
                    trait.authors,
                    trait.pubmed_text,
                    trait.LRS_score_repr,
                    trait.LRS_location_repr,
                    additive]
    elif dataset.type == "Geno":
        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                index,
                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
                trait.location_repr]
    else:
        return dict()


def retrieve_trait_info(trait, dataset, get_qtl_info=False):
    assert dataset, "Dataset doesn't exist"

    resource_id = get_resource_id(dataset, trait.name)
    if dataset.type == 'Publish':
        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
    else:
        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)

    try:
        response = requests.get(the_url).content
        if response.strip() == "no-access":
            trait.view = False
            return trait
        else:
            trait_info = json.loads(response)
    except:
        resource_info = get_resource_info(resource_id)
        if resource_info:
            default_permissions = resource_info['default_mask']['data']
        else:
            default_permissions = webqtlConfig.DEFAULT_PRIVILEGES
        if 'view' not in default_permissions:
            trait.view = False
            return trait

        if dataset.type == 'Publish':
            query = """
                    SELECT
                            PublishXRef.Id, Publication.PubMed_ID,
                            Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
                            Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
                            Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
                            Publication.Authors, Publication.Title, Publication.Abstract,
                            Publication.Journal, Publication.Volume, Publication.Pages,
                            Publication.Month, Publication.Year, PublishXRef.Sequence,
                            Phenotype.Units, PublishXRef.comments
                    FROM
                            PublishXRef, Publication, Phenotype, PublishFreeze
                    WHERE
                            PublishXRef.Id = %s AND
                            Phenotype.Id = PublishXRef.PhenotypeId AND
                            Publication.Id = PublishXRef.PublicationId AND
                            PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
                            PublishFreeze.Id = %s
                    """ % (trait.name, dataset.id)

            logger.sql(query)
            trait_info = g.db.execute(query).fetchone()

        #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
        #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
        elif dataset.type == 'ProbeSet':
            display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
            display_fields_string = 'ProbeSet.' + display_fields_string
            query = """
                    SELECT %s
                    FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
                    WHERE
                            ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
                            ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
                            ProbeSetFreeze.Name = '%s' AND
                            ProbeSet.Name = '%s'
                    """ % (escape(display_fields_string),
                        escape(dataset.name),
                        escape(str(trait.name)))
            logger.sql(query)
            trait_info = g.db.execute(query).fetchone()
        #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
        # to avoid the problem of same marker name from different species.
        elif dataset.type == 'Geno':
            display_fields_string = string.join(dataset.display_fields,',Geno.')
            display_fields_string = 'Geno.' + display_fields_string
            query = """
                    SELECT %s
                    FROM Geno, GenoFreeze, GenoXRef
                    WHERE
                            GenoXRef.GenoFreezeId = GenoFreeze.Id AND
                            GenoXRef.GenoId = Geno.Id AND
                            GenoFreeze.Name = '%s' AND
                            Geno.Name = '%s'
                    """ % (escape(display_fields_string),
                        escape(dataset.name),
                        escape(trait.name))
            logger.sql(query)
            trait_info = g.db.execute(query).fetchone()
        else: #Temp type
            query = """SELECT %s FROM %s WHERE Name = %s"""
            logger.sql(query)
            trait_info = g.db.execute(query,
                                    (string.join(dataset.display_fields,','),
                                                dataset.type, trait.name)).fetchone()

    if trait_info:
        trait.haveinfo = True

        for i, field in enumerate(dataset.display_fields):
            holder =  trait_info[i]
            if isinstance(trait_info[i], basestring):
                holder = holder.encode('latin1')
            setattr(trait, field, holder)

        if dataset.type == 'Publish':
            if trait.group_code:
                trait.display_name = trait.group_code + "_" + str(trait.name)

            trait.confidential = 0
            if trait.pre_publication_description and not trait.pubmed_id:
                trait.confidential = 1

            description = trait.post_publication_description

            #If the dataset is confidential and the user has access to confidential
            #phenotype traits, then display the pre-publication description instead
            #of the post-publication description
            if trait.confidential:
                trait.abbreviation = trait.pre_publication_abbreviation
                trait.description_display = trait.pre_publication_description
            else:
                trait.abbreviation = trait.post_publication_abbreviation
                if description:
                    trait.description_display = description.strip()
                else:
                    trait.description_display = ""

            trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
            trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
            trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")

            if not trait.year.isdigit():
                trait.pubmed_text = "N/A"
            else:
                trait.pubmed_text = trait.year

            if trait.pubmed_id:
                trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id

        if dataset.type == 'ProbeSet' and dataset.group:
            description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
            target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')

            if len(description_string) > 1 and description_string != 'None':
                description_display = description_string
            else:
                description_display = trait.symbol

            if (len(description_display) > 1 and description_display != 'N/A' and
                    len(target_string) > 1 and target_string != 'None'):
                description_display = description_display + '; ' + target_string.strip()

            # Save it for the jinja2 template
            trait.description_display = description_display

            trait.location_repr = 'N/A'
            if trait.chr and trait.mb:
                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))

        elif dataset.type == "Geno":
            trait.location_repr = 'N/A'
            if trait.chr and trait.mb:
                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))

        if get_qtl_info:
            #LRS and its location
            trait.LRS_score_repr = "N/A"
            trait.LRS_location_repr = "N/A"
            trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
            if dataset.type == 'ProbeSet' and not trait.cellid:
                trait.mean = ""
                query = """
                        SELECT
                                ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
                        FROM
                                ProbeSetXRef, ProbeSet
                        WHERE
                                ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
                                ProbeSet.Name = "{}" AND
                                ProbeSetXRef.ProbeSetFreezeId ={}
                        """.format(trait.name, dataset.id)
                logger.sql(query)
                trait_qtl = g.db.execute(query).fetchone()
                if trait_qtl:
                    trait.locus, trait.lrs, trait.pvalue, trait.mean, trait.additive = trait_qtl
                    if trait.locus:
                        query = """
                            select Geno.Chr, Geno.Mb from Geno, Species
                            where Species.Name = '{}' and
                            Geno.Name = '{}' and
                            Geno.SpeciesId = Species.Id
                            """.format(dataset.group.species, trait.locus)
                        logger.sql(query)
                        result = g.db.execute(query).fetchone()
                        if result:
                            trait.locus_chr = result[0]
                            trait.locus_mb = result[1]
                        else:
                            trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
                    else:
                        trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""

            if dataset.type == 'Publish':
                query = """
                        SELECT
                                PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive
                        FROM
                                PublishXRef, PublishFreeze
                        WHERE
                                PublishXRef.Id = %s AND
                                PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
                                PublishFreeze.Id =%s
                """ % (trait.name, dataset.id)
                logger.sql(query)
                trait_qtl = g.db.execute(query).fetchone()
                if trait_qtl:
                    trait.locus, trait.lrs, trait.additive = trait_qtl
                    if trait.locus:
                        query = """
                            select Geno.Chr, Geno.Mb from Geno, Species
                            where Species.Name = '{}' and
                            Geno.Name = '{}' and
                            Geno.SpeciesId = Species.Id
                            """.format(dataset.group.species, trait.locus)
                        logger.sql(query)
                        result = g.db.execute(query).fetchone()
                        if result:
                            trait.locus_chr = result[0]
                            trait.locus_mb = result[1]
                        else:
                            trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
                    else:
                        trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
                else:
                    trait.locus = trait.lrs = trait.additive = ""

            if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
                trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
                if trait.lrs != "":
                    trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
    else:
        raise KeyError, `trait.name`+' information is not found in the database.'
        
    return trait