MAJ terminée. Nous sommes passés en version 14.6.2 . Pour consulter les "releases notes" associées c'est ici :

https://about.gitlab.com/releases/2022/01/11/security-release-gitlab-14-6-2-released/
https://about.gitlab.com/releases/2022/01/04/gitlab-14-6-1-released/

fuse.py 26.8 KB
Newer Older
1
2
3
4
5
#!/usr/bin/env python
# -*- coding: utf-8 -*-

### fuse.py - Vidjil utility to parse and regroup list of clones of different timepoints or origins

6
7
#  This file is part of Vidjil <http://www.vidjil.org>,
#  High-throughput Analysis of V(D)J Immune Repertoire.
8
#  Copyright (C) 2011-2017 by Bonsai bioinformatics
9
10
11
12
13
#  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
#  Contributors: 
#      Marc Duez <marc.duez@vidjil.org>
#      Mathieu Giraud <mathieu.giraud@vidjil.org>
#      The Vidjil Team <contact@vidjil.org>
14
15
16
17
18
19
20
21
22
23
24
25
26
27
#
#  "Vidjil" is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#
#  "Vidjil" is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  You should have received a copy of the GNU General Public License
#  along with "Vidjil". If not, see <http://www.gnu.org/licenses/>

Mathieu Giraud's avatar
Mathieu Giraud committed
28
from __future__ import print_function
29

30
import check_python_version
31
import sys
32
33
import json
import argparse
34
import os.path
Mikaël Salson's avatar
Mikaël Salson committed
35
import os
Marc Duez's avatar
Marc Duez committed
36
import datetime
37
import subprocess
38
import tempfile
39
from operator import itemgetter, le
40
from utils import *
41
from defs import *
42
from collections import defaultdict
43

44
45
from vidjilparser import VidjilParser

46
FUSE_VERSION = "vidjil fuse"
47

48
TOOL_SIMILARITY = "../algo/tools/similarity"
49
SIMILARITY_LIMIT = 100
50

51
52
GERMLINES_ORDER = ['TRA', 'TRB', 'TRG', 'TRD', 'DD', 'IGH', 'DHJH', 'IJK', 'IJL'] 

53
54
55
####

class Window:
56
    # Should be renamed "Clone"
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
    '''storage class for sequence informations
    with some function to group sequence informations
    
    >>> str(w1)
    '<window : [5] 3 aaa>'
    
    >>> str(w3)
    '<window : [8] 4 aaa>'
    
    >>> str(w1 + w3)
    '<window : [5, 8] 3 aaa>'
    
    
    check if other information are conserved
    
    >>> (w2 + w4).d["test"]
    [0, 'plop']
    
    '''
    
    ### init Window with the minimum data required
    def __init__(self, size):
        self.d={}
80
        self.d["id"] = ""
Mathieu Giraud's avatar
Mathieu Giraud committed
81
        self.d["top"] = sys.maxsize
82
        self.d["reads"] = []
83
        for i in range(size):
84
            self.d["reads"].append(0)
85
86
87
        
        
    ### 
88
89
    def __iadd__(self, other):
        ### Not used now
90
        """Add other.reads to self.reads in-place, without extending lists"""
91

92
93
        assert(len(self.d['reads']) == len(other.d['reads']))
        self.d['reads'] = [my + her for (my, her) in zip(self.d['reads'], other.d['reads'])]
94
95
96

        return self
        
97
    def __add__(self, other):
98
        """Concat two windows, extending lists such as 'reads'"""
99
        #data we don't need to duplicate
100
        myList = [ "seg", "top", "id", "sequence", "name", "id", "stats", "germline"]
101
102
        obj = Window(1)
        
103
104
105
106
        concatenate_with_padding(obj.d,
                                 self.d, len(self.d["reads"]),
                                 other.d, len(other.d["reads"]),
                                 myList)
107
108
                    
        #keep other data who don't need to be concat
109
        if other.d["top"] < self.d["top"] :
110
111
112
113
114
115
116
117
118
119
            for key in other.d :
                if key in myList :
                    obj.d[key] = other.d[key]
        else :
            for key in self.d :
                if key in myList :
                    obj.d[key] = self.d[key]
        
        return obj
        
120
121
    def get_nb_reads(self, cid, point=0):
        return self[cid]["reads"][point]
122

123
    def latex(self, point=0, base_germline=10000, base=10000, tag=''):
124
        reads = self.d["reads"][point]
125
        ratio_germline = float(reads)/base_germline
126
        ratio = float(reads)/base
127
        return r"   &   & %7d & %5.2f\%% & of %-4s & %5.2f\%% & %-50s \\ %% %4s %s" % (reads, ratio_germline * 100, self.d['germline'], ratio * 100,
128
129
                                                                  self.d["name"] if 'name' in self.d else self.d["id"],
                                                                  tag, self.d["id"])
130

131
132
    ### print essential info about Window
    def __str__(self):
Mathieu Giraud's avatar
Mathieu Giraud committed
133
        return "<window : %s %s %s>" % ( self.d["reads"], '*' if self.d["top"] == sys.maxsize else self.d["top"], self.d["id"])
134
        
Marc Duez's avatar
Marc Duez committed
135
class Samples: 
136

Marc Duez's avatar
Marc Duez committed
137
138
    def __init__(self):
        self.d={}
139
        self.d["number"] = 1
Marc Duez's avatar
Marc Duez committed
140
141
142
143
        self.d["original_names"] = [""]

    def __add__(self, other):
        obj=Samples()
144

145
146
147
148
149
        concatenate_with_padding(obj.d, 
                                 self.d, self.d['number'], 
                                 other.d, other.d['number'],
                                 ['number'])

150
        obj.d["number"] =  int(self.d["number"]) + int(other.d["number"])
Marc Duez's avatar
Marc Duez committed
151
152
        
        return obj
153

154
155
156
    def __str__(self):
        return "<Samples: %s>" % self.d

157
158
class Diversity: 

159
160
    keys = ["index_H_entropy", "index_E_equitability", "index_Ds_diversity"]

161
162
163
    def __init__(self, data=None):
        self.d={}

164
165
166
167
168
        for k in self.keys:
            if data == None or not (k in data):
                self.d[k] = ["na"]
            else:
                self.d[k]= [data[k]]
169

170
171
172
    def __add__(self, other):
        for k in self.keys:
            self.d[k].append(other.d[k][0])
173
174
175
176
177
        return self

    def __str__(self):
        return "<Diversity: %s>" % self.d
        
178
179
180
181
182
183
184
class Reads: 

    def __init__(self):
        self.d={}
        self.d["total"] = ["0"]
        self.d["segmented"] = ["0"]
        self.d["germline"] = {}
185
        self.d['distribution'] = {}
186
187
188

    def __add__(self, other):
        obj=Reads()
189
190
191
192
193

        concatenate_with_padding(obj.d['germline'], 
                                 self.d['germline'], len(self.d['total']),
                                 other.d['germline'], len(other.d['total']),
                                 ['total'])
194
195
196
197
        concatenate_with_padding(obj.d['distribution'],
                                 self.d['distribution'], len(self.d['total']),
                                 other.d['distribution'], len(other.d['total']),
                                 ['total'])
198
199
200
201
                
        obj.d["total"] = self.d["total"] + other.d["total"]
        obj.d["segmented"] = self.d["segmented"] + other.d["segmented"]
        return obj
202
203
204

    def __str__(self):
        return "<Reads: %s>" % self.d
205
        
206
207
208
209
class OtherWindows:
    
    """Aggregate counts of windows that are discarded (due to too small 'top') for each point into several 'others-' windows."""

210
211
    def __init__(self, length, ranges = None):
        self.ranges = ranges if ranges is not None else [1000, 100, 10, 1]
212
213
214
215
216
217
218
219
220
221
        self.length = length
        self.sizes = {}

        for r in self.ranges:
            self.sizes[r] = [0 for i in range(self.length)]


    def __iadd__(self, window):
        """Add to self a window. The different points may land into different 'others-' windows."""

222
        for i, s in enumerate(window.d["reads"]):
223
224
225
226
227
            for r in self.ranges:
                if s >= r:
                     break
            self.sizes[r][i] += s
            ## TODO: add seg_stat
228
229
            
        # print window, '-->', self.sizes
230
231
232
233
234
235
236
        return self

    def __iter__(self):
        """Yield the 'others-' windows"""

        for r in self.ranges:
            w = Window(self.length)
237
            w.d['reads'] = self.sizes[r]
238
239
240
            w.d['window'] = 'others-%d' % r
            w.d['top'] = 0

Mathieu Giraud's avatar
Mathieu Giraud committed
241
            print('  --[others]-->', w)
242
            yield w
243
        
244
class ListWindows(VidjilJson):
245
246
247
    '''storage class for sequences informations 
    
    >>> lw1.info()
Mathieu Giraud's avatar
Mathieu Giraud committed
248
    <ListWindows: [25] 2>
249
250
251
252
    <window : [5] 3 aaa>
    <window : [12] 2 bbb>
    
    >>> lw2.info()
Mathieu Giraud's avatar
Mathieu Giraud committed
253
    <ListWindows: [34] 2>
254
255
256
    <window : [8] 4 aaa>
    <window : [2] 8 ccc>
    
Mathieu Giraud's avatar
Mathieu Giraud committed
257
    >>> lw3 = lw1 + lw2
258
    >>> lw3.info()
Mathieu Giraud's avatar
Mathieu Giraud committed
259
    <ListWindows: [25, 34] 3>
260
261
262
    <window : [12, 0] 2 bbb>
    <window : [5, 8] 3 aaa>
    <window : [0, 2] 8 ccc>
263
264
265
266
267
268
269
270
271
272
    >>> lw3.build_stat()
    >>> lw3.d['reads'].d['distribution']['0.1']
    [17, 8]
    >>> lw3.d['reads'].d['distribution']['0.01']
    [0, 2]
    >>> lw3.d['reads'].d['distribution']['0.001']
    [0, 0]
    >>> lw3.d['reads'].d['distribution']['0.0001']
    [0, 0]

273
274
275
276
277
    '''
    
    def __init__(self):
        '''init ListWindows with the minimum data required'''
        self.d={}
278
279
        self.d["samples"] = Samples()
        self.d["reads"] = Reads()
280
281
        self.d["clones"] = []
        self.d["clusters"] = []
282
        self.d["germlines"] = {}
283
        
284
285
286
287
        self.d["vidjil_json_version"] = VIDJIL_JSON_VERSION
        self.d["producer"] = FUSE_VERSION
        self.d["timestamp"] = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
        
288
    def __str__(self):
289
290
291
292
293
294
295
296
297
298
299
300
301
302
        return "<ListWindows: %s %d>" % ( self.d["reads"].d["segmented"], len(self) )

    # Iterator and access functions
    def __iter__(self):
        return self.d["clones"].__iter__()

    def __getitem__(self, i):
        ### not efficient !
        for clone in self:
            if clone.d["id"] == i:
                return clone

    def __len__(self):
        return len(self.d["clones"])
303
304
305

    ### print info about each Windows stored 
    def info(self):
Mathieu Giraud's avatar
Mathieu Giraud committed
306
        print(self)
307
        for clone in self:
Mathieu Giraud's avatar
Mathieu Giraud committed
308
            print(clone)
309
        
310
311
    ### compute statistics about clones
    def build_stat(self):
312
        ranges = [.1, .01, .001, .0001, .00001, .000001, .0000001]
313
        result = [[0 for col in range(len(self.d['reads'].d["segmented"]))] for row in range(len(ranges))]
314

315
316
        for clone in self:
            for i, s in enumerate(clone.d["reads"]):
317
                for r in range(len(ranges)):
318
                    if s*1. / self.d['reads'].d['segmented'][i] >= ranges[r]:
319
320
321
322
                        break 
                result[r][i] += s
                
        for r in range(len(ranges)):
323
324
            ratio_in_string = '{0:.10f}'.format(ranges[r]).rstrip('0')
            self.d['reads'].d['distribution'][ratio_in_string] = result[r]
325
326
327
328
            
        #TODO V/D/J distrib and more 
        
        
329
330
331
    ### save / load to .json
    def save_json(self, output):
        '''save ListWindows in .json format''' 
Mathieu Giraud's avatar
Mathieu Giraud committed
332
        print("==>", output)
333
334
        with open(output, "w") as f:
            json.dump(self, f, indent=2, default=self.toJson)
335

336
    def load(self, file_path, *args, **kwargs):
337
338
339
340
        if not '.clntab' in file_path:
            self.load_vidjil(file_path, *args, **kwargs)
        else:
            self.load_clntab(file_path, *args, **kwargs)
341
342
343
344
345
346

    def loads(self, string, *args, **kwargs):
        self.loads_vidjil(string, *args, **kwargs)

    def init_data(self, data):
        self.d=data.d
347
348
349
        # Be robust against 'null' values for clones
        if not self.d["clones"]:
            self.d["clones"] = []
350

351
352
353
354
        if "diversity" in self.d.keys():
            self.d["diversity"] = Diversity(self.d["diversity"])
        else:
            self.d["diversity"] = Diversity()
355
        
356
357
        if 'distribution' not in self.d['reads'].d:
            self.d['reads'].d['distribution'] = {}
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381

        self.id_lengths = defaultdict(int)

        print("%%")
        for clone in self:
            self.id_lengths[len(clone.d['id'])] += 1
        print ("%% lengths .vidjil -> ", self.id_lengths)
        try:
            print("%% run_v ->", self.d["samples"].d["producer"], self.d["samples"].d["run_timestamp"])
        except KeyError:
            pass

    def load_vidjil(self, file_path, pipeline, verbose=True):
        '''init listWindows with data file
        Detects and selects the parser according to the file extension.'''
        extension = file_path.split('.')[-1]

        if verbose:
            print("<==", file_path, "\t", end=' ')

        with open(file_path, "r") as f:
            self.init_data(json.load(f, object_hook=self.toPython))
            self.check_version(file_path)

382
383
384
        if pipeline: 
            # renaming, private pipeline
            f = '/'.join(file_path.split('/')[2:-1])
385
            if verbose:
Mathieu Giraud's avatar
Mathieu Giraud committed
386
                print("[%s]" % f)
387
388
389

        else:
            f = file_path
390
            if verbose:
Mathieu Giraud's avatar
Mathieu Giraud committed
391
                print()
392

Marc Duez's avatar
Marc Duez committed
393
        time = os.path.getmtime(file_path)
394
        self.d["samples"].d["timestamp"] = [datetime.datetime.fromtimestamp(time).strftime("%Y-%m-%d %H:%M:%S")]
395

396
397
398
    def loads_vidjil(self, string, pipeline, verbose=True):
        '''init listWindows with a json string'''
        self.init_data(json.loads(string, object_hook=self.toPython))
399

Marc Duez's avatar
Marc Duez committed
400
401
402
    def getTop(self, top):
        result = []
        
403
404
405
        for clone in self:
            if clone.d["top"] <= top :
                result.append(clone.d["id"])
Marc Duez's avatar
Marc Duez committed
406
407
408
409
410
        return result
        
    def filter(self, f):
        r = []
        
Marc Duez's avatar
Marc Duez committed
411
        reverseList = {}
412
413
        for i,w in enumerate(self.d["clones"]) :
            reverseList[w.d["id"]] = i
Marc Duez's avatar
Marc Duez committed
414
415
416
        
        #filteredList = { k: reverseList[k] for k in f }
        filteredList = dict(filter(lambda t: t[0] in f, reverseList.items()))
Marc Duez's avatar
Marc Duez committed
417
        
Marc Duez's avatar
Marc Duez committed
418
        for i in filteredList:
419
            r.append(self.d["clones"][filteredList[i]])
Marc Duez's avatar
Marc Duez committed
420
        
421
        self.d["clones"] = r
Marc Duez's avatar
Marc Duez committed
422
        
423
424
425
426
    ### 
    def __add__(self, other): 
        '''Combine two ListWindows into a unique ListWindows'''
        obj = ListWindows()
427
428
        l1 = len(self.d["reads"].d['segmented'])
        l2 = len(other.d["reads"].d['segmented'])
429

430
431
432
        concatenate_with_padding(obj.d, 
                                 self.d, l1,
                                 other.d, l2,
433
434
                                 ["clones", "links", "germlines",
                                  "vidjil_json_version"])
435
        
436
        obj.d["clones"]=self.fuseWindows(self.d["clones"], other.d["clones"], l1, l2)
437
438
        obj.d["samples"] = self.d["samples"] + other.d["samples"]
        obj.d["reads"] = self.d["reads"] + other.d["reads"]
439
        obj.d["diversity"] = self.d["diversity"] + other.d["diversity"]
440
        
441
442
        return obj
        
443
444
445
446
447
448
    ###
    def __mul__(self, other):
        
        for i in range(len(self.d["reads_segmented"])):
            self.d["reads_segmented"][i] += other.d["reads_segmented"][i] 
        
449
        self.d["clones"] += other.d["clones"]
450
451
452
453
454
455
        self.d["vidjil_json_version"] = [VIDJIL_JSON_VERSION]
        
        self.d["system_segmented"].update(other.d["system_segmented"])
        
        return self
        
456
    ### 
457
    def fuseWindows(self, w1, w2, l1, l2) :
458
        #store data in dict with "id" as key
459
460
        dico1 = {}
        for i in range(len(w1)) :
461
            dico1[ w1[i].d["id"] ] = w1[i]
462
463
464

        dico2 = {}
        for i in range(len(w2)) :
465
            dico2[ w2[i].d["id"] ] = w2[i]
466

467
        #concat data with the same key ("id")
468
469
470
471
472
473
        #if some data are missing we concat with an empty Windows()
        dico3 = {}
        for key in dico1 :
            if key in dico2 :
                dico3[key] = dico1[key] + dico2[key]
            else :
474
                w=Window(l2)
475
476
477
478
                dico3[key] = dico1[key] + w

        for key in dico2 :
            if key not in dico1 :
479
                w=Window(l1)
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
                dico3[key] = w + dico2[key]
        
        
        #sort by top
        tab = []
        for key in dico3 :
            tab.append((dico3[key], dico3[key].d["top"]))
        tab = sorted(tab, key=itemgetter(1))
        
        #store back in a List
        result=[]
        for i in range(len(tab)) :
            result.append(tab[i][0])
        
        return result
        
    
497
498
    def cut(self, limit, nb_points):
        '''Remove information from sequence/windows who never enter in the most represented sequences. Put this information in 'other' windows.'''
499
500

        w=[]
501
502
503

        others = OtherWindows(nb_points)

504
505
506
        for clone in self:
            if (int(clone.d["top"]) < limit or limit == 0) :
                w.append(clone)
507
            #else:
508
                #others += clone
509

510
        self.d["clones"] = w #+ list(others) 
511

Mathieu Giraud's avatar
Mathieu Giraud committed
512
        print("### Cut merged file, keeping window in the top %d for at least one point" % limit)
513
514
        return self
        
515
    def load_clntab(self, file_path, *args, **kwargs):
516
517
518
        '''Parser for .clntab file'''

        self.d["vidjil_json_version"] = [VIDJIL_JSON_VERSION]
519
        self.d["samples"].d["original_names"] = [file_path]
520
        self.d["samples"].d["producer"] = ["EC-NGS central pipeline"]
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
        
        listw = []
        listc = []
        total_size = 0
        
        fichier = open(file_path,"r")
        for ligne in fichier:
            if "clonotype" in ligne:
                header_map = ligne.replace('\n', '').split('\t')
            else :
                tab = AccessedDict()
                for index, data in enumerate(ligne.split('\t')):
                    tab[header_map[index]] = data
                        
                w=Window(1)
536
537
                w.d["seg"] = {}
                
538
                #w.window=tab["sequence.seq id"] #use sequence id as window for .clntab data
539
                w.d["id"]=tab["sequence.raw nt seq"] #use sequence as window for .clntab data
540
541
                s = int(tab["sequence.size"])
                total_size += s
542
                w.d["reads"] = [ s ]
543

544
545
                w.d["germline"] = tab["sequence.V-GENE and allele"][:3] #system ...
                
546
                w.d["sequence"] = tab["sequence.raw nt seq"]
547
                w.d["seg"]["5"]=tab["sequence.V-GENE and allele"].split('=')[0]
548
                if (tab["sequence.D-GENE and allele"] != "") :
549
550
                    w.d["seg"]["4"]=tab["sequence.D-GENE and allele"].split('=')[0]
                w.d["seg"]["3"]=tab["sequence.J-GENE and allele"].split('=')[0]
551
552
553
554

                # use sequence.JUNCTION to colorize output (this is not exactly V/J !)
                junction = tab.get("sequence.JUNCTION.raw nt seq")
                position = w.d["sequence"].find(junction)
555
                
556
                if position >= 0:
557
558
                    w.d["seg"]["3start"] = position + len(junction)
                    w.d["seg"]["5end"] = position 
559
                else:
560
561
562
563
564
565
                    w.d["seg"]["3start"] = 0
                    w.d["seg"]["5end"] = len(w.d["sequence"])
                w.d["seg"]["3end"]=0
                w.d["seg"]["5start"]=0
                w.d["seg"]["4end"]=0
                w.d["seg"]["4start"]=0
566
                w.d["seg"]["cdr3"] = tab["sequence.JUNCTION.raw nt seq"][3:-3]
567
                    
568
                listw.append((w , w.d["reads"][0]))
569
570

                raw_clonotype = tab.get("clonotype")
571
572
                w.d["name"]=raw_clonotype # w.d["seg"]["5"] + " -x/y/-z " + w.d["seg"]["3"]

573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
                clonotype = raw_clonotype.split(' ')
                if (len(clonotype) > 1) :
                    listc.append((w, raw_clonotype))
                
                #keep data that has not already been stored
                for header in tab.not_accessed_keys():
                    w.d["_"+header] = [tab[header]]

        #sort by sequence_size
        listw = sorted(listw, key=itemgetter(1), reverse=True)
        #sort by clonotype
        listc = sorted(listc, key=itemgetter(1))
        
        #generate data "top"
        for index in range(len(listw)):
            listw[index][0].d["top"]=index+1
589
            self.d["clones"].append(listw[index][0])
590
        
591
592
        self.d["reads"].d["segmented"] = [total_size]
        self.d["reads"].d["total"] = [total_size]
593
594
595
596

        
    def toJson(self, obj):
        '''Serializer for json module'''
597
        if isinstance(obj, ListWindows) or isinstance(obj, Window) or isinstance(obj, Samples) or isinstance(obj, Reads) or isinstance(obj, Diversity):
598
599
600
            result = {}
            for key in obj.d :
                result[key]= obj.d[key]
Marc Duez's avatar
Marc Duez committed
601
                
602
603
            return result
            raise TypeError(repr(obj) + " fail !") 
604
        
Marc Duez's avatar
Marc Duez committed
605
        else:
606
607
608
609
610
611
            result = {}
            for key in obj :
                result[key]= obj[key]
            
            return result
            raise TypeError(repr(obj) + " fail !") 
612
613
614

    def toPython(self, obj_dict):
        '''Reverse serializer for json module'''
615
        if "samples" in obj_dict:
616
            obj = ListWindows()
617
            obj.d=obj_dict
618
619
            return obj

620
        if "id" in obj_dict:
621
            obj = Window(1)
622
            obj.d=obj_dict
623
            return obj
Marc Duez's avatar
Marc Duez committed
624
        
625
626
        if "total" in obj_dict:
            obj = Reads()
627
            obj.d=obj_dict
628
629
            return obj
            
Marc Duez's avatar
Marc Duez committed
630
631
        if "original_names" in obj_dict:
            obj = Samples()
632
            obj.d=obj_dict
633
            return obj
Marc Duez's avatar
Marc Duez committed
634
            
635
        return obj_dict
636
637
638
639
640
641
        



### some data used for test
w1 = Window(1)
642
w1.d ={"id" : "aaa", "reads" : [5], "top" : 3 }
643
w2 = Window(1)
644
w2.d ={"id" : "bbb", "reads" : [12], "top" : 2 }
645
w3 = Window(1)
646
w3.d ={"id" : "aaa", "reads" : [8], "top" : 4 }
647
w4 = Window(1)
648
w4.d ={"id" : "ccc", "reads" : [2], "top" : 8, "test" : ["plop"] }
649
650
651


w5 = Window(1)
652
w5.d ={"id" : "aaa", "reads" : [5], "top" : 3 }
653
w6 = Window(1)
654
w6.d ={"id" : "bbb", "reads" : [12], "top" : 2 }
655
656

lw1 = ListWindows()
657
lw1.d["timestamp"] = 'ts'
658
lw1.d["reads"] = json.loads('{"total": [30], "segmented": [25], "germline": {}, "distribution": {}}', object_hook=lw1.toPython)
659
660
lw1.d["clones"].append(w5)
lw1.d["clones"].append(w6)
661
662
lw1.d["diversity"] = Diversity()

663
664

w7 = Window(1)
665
w7.d ={"id" : "aaa", "reads" : [8], "top" : 4 }
666
w8 = Window(1)
667
w8.d ={"id" : "ccc", "reads" : [2], "top" : 8, "test" : ["plop"] }
668
669

lw2 = ListWindows()
670
lw2.d["timestamp"] = 'ts'
671
lw2.d["reads"] = json.loads('{"total": [40], "segmented": [34], "germline": {}, "distribution": {}}', object_hook=lw1.toPython)
672
673
lw2.d["clones"].append(w7)
lw2.d["clones"].append(w8)
674
lw2.d["diversity"] = Diversity()
675
676
677
678
679
680

    
    

 
def main():
Mathieu Giraud's avatar
Mathieu Giraud committed
681
    print("#", ' '.join(sys.argv))
682
683
684
685
686
687
688

    DESCRIPTION = 'Vidjil utility to parse and regroup list of clones of different timepoints or origins'
    
    #### Argument parser (argparse)

    parser = argparse.ArgumentParser(description= DESCRIPTION,
                                    epilog='''Example:
Mathieu Giraud's avatar
Mathieu Giraud committed
689
  python2 %(prog)s --germline IGH out/Diag/vidjil.data out/MRD-1/vidjil.data out/MRD-2/vidjil.data''',
690
691
692
693
694
695
                                    formatter_class=argparse.RawTextHelpFormatter)


    group_options = parser.add_argument_group() # title='Options and parameters')

    group_options.add_argument('--test', action='store_true', help='run self-tests')
696
    group_options.add_argument('--multi', action='store_true', help='merge different systems from a same timepoint (deprecated, do not use)')
697
    
698
    group_options.add_argument('--compress', '-c', action='store_true', help='compress point names, removing common substrings')
699
    group_options.add_argument('--pipeline', '-p', action='store_true', help='compress point names (internal Bonsai pipeline)')
700
    group_options.add_argument('--ijson', action='store_true', help='use the ijson vidjilparser')
701

Marc Duez's avatar
Marc Duez committed
702
    group_options.add_argument('--output', '-o', type=str, default='fused.vidjil', help='output file (%(default)s)')
703
704
    group_options.add_argument('--top', '-t', type=int, default=50, help='keep only clones in the top TOP of some point (%(default)s)')

705
    group_options.add_argument('--first', '-f', type=int, default=0, help='take only into account the first FIRST files (0 for all) (%(default)s)')
706

707
708
709
710
711
712
713
714
715
716
717
718
    parser.add_argument('file', nargs='+', help='''input files (.vidjil/.cnltab)''')
  
    args = parser.parse_args()
    # print args

    if args.test:
        import doctest
        doctest.testmod(verbose = True)
        sys.exit(0)

    jlist_fused = None

Mathieu Giraud's avatar
Mathieu Giraud committed
719
720
    print("### fuse.py -- " + DESCRIPTION)
    print()
721

722
723
724
725
726
727
    files = args.file
    if args.first:
        if len(files) > args.first:
            print("! %d files were given. We take into account the first %d files." % (len(files), args.first))
        files = files[:args.first]

Marc Duez's avatar
Marc Duez committed
728
729
    #filtre
    f = []
730
731

    vparser = VidjilParser()
732
    vparser.addPrefix('clones.item', 'clones.item.top', le, args.top)
733
    for path_name in files:
734
735
736
737
738
739
740
741
742
        if args.ijson:
            json_clones = vparser.extract(path_name)
            clones = json.loads(json_clones)
            f += [c['id'] for c in clones["clones"]]
        else:
            jlist = ListWindows()
            jlist.load(path_name, args.pipeline)
            f += jlist.getTop(args.top)

Marc Duez's avatar
Marc Duez committed
743
744
    f = sorted(set(f))
    
745
746
747
748
749
    if args.ijson:
        vparser.reset()
        vparser.addPrefix('')
        vparser.addPrefix('clones.item', 'clones.item.id', (lambda x, y: x in y), f)

750
    if args.multi:
751
        for path_name in files:
752
            jlist = ListWindows()
753
754
755
756
757
758
            if args.ijson:
                json_reads = vparser.extract(path_name)
                jlist.loads(json_reads, args.pipeline)
            else:
                jlist.load(path_name, args.pipeline)
                jlist.build_stat()
759
            
Mathieu Giraud's avatar
Mathieu Giraud committed
760
            print("\t", jlist, end=' ')
761
762
763
764
765

            if jlist_fused is None:
                jlist_fused = jlist
            else:
                jlist_fused = jlist_fused * jlist
766
                
Mathieu Giraud's avatar
Mathieu Giraud committed
767
            print('\t==> merge to', jlist_fused)
768
        jlist_fused.d["system_segmented"] = ordered(jlist_fused.d["system_segmented"], key=lambda sys: ((GERMLINES_ORDER + [sys]).index(sys), sys))
769
        
770
    else:
Mathieu Giraud's avatar
Mathieu Giraud committed
771
        print("### Read and merge input files")
772
        for path_name in files:
773
            jlist = ListWindows()
774
775
776
777
778
779
780
            if args.ijson:
                json_reads = vparser.extract(path_name)
                jlist.loads(json_reads, args.pipeline)
            else:
                jlist.load(path_name, args.pipeline)
                jlist.build_stat()
                jlist.filter(f)
Marc Duez's avatar
Marc Duez committed
781

782
783
784
785
            w1 = Window(1)
            w2 = Window(2)
            w3 = w1+w2
            
Mathieu Giraud's avatar
Mathieu Giraud committed
786
            print("\t", jlist, end=' ')
787
788
789
790
791
            # Merge lists
            if jlist_fused is None:
                jlist_fused = jlist
            else:
                jlist_fused = jlist_fused + jlist
792
            
Mathieu Giraud's avatar
Mathieu Giraud committed
793
            print('\t==> merge to', jlist_fused)
794

795
    if args.compress:
Mathieu Giraud's avatar
Mathieu Giraud committed
796
797
        print()
        print("### Select point names")
798
        l = jlist_fused.d["samples"].d["original_names"]
799
        ll = interesting_substrings(l)
Mathieu Giraud's avatar
Mathieu Giraud committed
800
801
        print("  <==", l)
        print("  ==>", ll)
802
        jlist_fused.d["samples"].d["names"] = ll
803
    
Mathieu Giraud's avatar
Mathieu Giraud committed
804
    print()
805
    if not args.multi:
806
        jlist_fused.cut(args.top, jlist_fused.d["samples"].d["number"])
Mathieu Giraud's avatar
Mathieu Giraud committed
807
808
    print("\t", jlist_fused) 
    print()
809

810
    #compute similarity matrix
811
812
813
814
815
    if len(jlist_fused.d["clones"]) < SIMILARITY_LIMIT :
        fasta = ""
        for i in range(len(jlist_fused.d["clones"])) :
            fasta += ">>" + str(i) + "\n"
            fasta += jlist_fused.d["clones"][i].d["id"] + "\n"
Ryan Herbert's avatar
Ryan Herbert committed
816
        fasta_file = tempfile.NamedTemporaryFile(mode="w", delete=False)
817
818
819
820
821
822
        fasta_file.write(fasta)
        try:
            out = subprocess.check_output([TOOL_SIMILARITY, "-j", fasta_file.name])
            jlist_fused.d["similarity"] = json.loads(out)
        except OSError:
            print("! failed: %s" % TOOL_SIMILARITY)
823
824
        finally:
            os.unlink(fasta_file.name)
825
826
    else : 
        jlist_fused.d["similarity"] = [];
827
        
Mathieu Giraud's avatar
Mathieu Giraud committed
828
    print("### Save merged file")
829
    jlist_fused.save_json(args.output)
830
    
831
832
833
834
    
    
if  __name__ =='__main__':
    main()