-
Notifications
You must be signed in to change notification settings - Fork 0
/
process.py
623 lines (482 loc) · 27.5 KB
/
process.py
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
# merge counts files into a data table, combine reads from multiple sequencing runs,
# filter by read counts, generate phenotype scores, average replicates
import pandas as pd
import os
import sys
import numpy as np
import scipy as sp
from scipy import stats
import fnmatch
import argparse
from config import parseExptConfig, parseLibraryConfig
from counts import makeDirectory, printNow
import analysis as screen_analysis
defaultLibConfigName = 'library_config.txt'
# a screen processing pipeline that requires just a config file and a directory of supported libraries
# error checking in config parser is fairly robust, so not checking for input errors here
def processExperimentsFromConfig(libraryDirectory):
print("starting experimental processing here...")
generatePlots='png'
configFile='config.ini'
# load in the supported libraries and sublibraries
try:
librariesToSublibraries, librariesToTables = parseLibraryConfig(
os.path.join(libraryDirectory, defaultLibConfigName))
except ValueError as err:
print(' '.join(err.args))
return
exptParameters, parseStatus, parseString = parseExptConfig(
configFile, librariesToSublibraries)
printNow(parseString)
if parseStatus > 0: # Critical errors in parsing
print('Exiting due to experiment config file errors\n')
return
makeDirectory(exptParameters['output_folder'])
outbase = os.path.join(
exptParameters['output_folder'], exptParameters['experiment_name'])
if generatePlots != 'off':
plotDirectory = os.path.join(
exptParameters['output_folder'], exptParameters['experiment_name'] + '_plots')
makeDirectory(plotDirectory)
screen_analysis.changeDisplayFigureSettings(
newDirectory=plotDirectory, newImageExtension=generatePlots, newPlotWithPylab=False)
# load in library table and filter to requested sublibraries
printNow('Accessing library information')
libraryTable = pd.read_csv(os.path.join(
libraryDirectory, librariesToTables[exptParameters['library']]), sep='\t', header=0, index_col=0).sort_index()
sublibColumn = libraryTable.apply(
lambda row: row['sublibrary'].lower() in exptParameters['sublibraries'], axis=1)
if sum(sublibColumn) == 0:
print('After limiting analysis to specified sublibraries, no elements are left')
return
libraryTable[sublibColumn].to_csv(outbase + '_librarytable.txt', sep='\t')
# load in counts, create table of total counts in each and each file as a column
printNow('Loading counts data')
# TODO: Fix issues here with column name creation
columnDict = dict()
for tup in sorted(exptParameters['counts_file_list']):
if tup in columnDict:
print('Asserting that tuples of condition, replicate, and count file should be unique; are the cases where this should not be enforced?')
raise Exception(
'condition, replicate, and count file combination already assigned')
# for now also dropping duplicate ids in counts for overlapping linc sublibraries
countSeries = readCountsFile(tup[2]).reset_index(
).drop_duplicates('id').set_index('id')
countSeries = libraryTable[sublibColumn].align(countSeries, axis=0, join='left', fill_value=0)[
1] # expand series to fill 0 for every missing entry
# [sublibColumn] #then shrink series to only desired sublibraries
columnDict[tup] = countSeries['counts']
# print columnDict
# , index=libraryTable[sublibColumn].index)
countsTable = pd.DataFrame(columnDict)
countsTable.to_csv(outbase + '_rawcountstable.txt', sep='\t')
countsTable.sum().to_csv(outbase + '_rawcountstable_summary.txt', sep='\t', header=False)
# merge counts for same conditions/replicates, and create summary table
# save scatter plot before each merger, and histogram of counts post mergers
printNow('Merging experiment counts split across lanes/indexes')
exptGroups = countsTable.groupby(level=[0, 1], axis=1)
mergedCountsTable = exptGroups.aggregate(np.sum)
mergedCountsTable.to_csv(outbase + '_mergedcountstable.txt', sep='\t')
mergedCountsTable.sum().to_csv(
outbase + '_mergedcountstable_summary.txt', sep='\t', header=False)
if generatePlots != 'off' and max(exptGroups.count().iloc[0]) > 1:
printNow('-generating scatter plots of counts pre-merger')
tempDataDict = {'library': libraryTable[sublibColumn],
'premerged counts': countsTable,
'counts': mergedCountsTable}
for (phenotype, replicate), countsCols in exptGroups:
if len(countsCols.columns) == 1:
continue
else:
screen_analysis.premergedCountsScatterMatrix(
tempDataDict, phenotype, replicate)
if generatePlots != 'off':
printNow('-generating sgRNA read count histograms')
tempDataDict = {'library': libraryTable[sublibColumn],
'counts': mergedCountsTable}
for (phenotype, replicate), countsCol in mergedCountsTable.items():
screen_analysis.countsHistogram(tempDataDict, phenotype, replicate)
# create pairs of columns for each comparison, filter to na, then generate sgRNA phenotype score
printNow('Computing sgRNA phenotype scores')
growthValueDict = {(tup[0], tup[1]): tup[2]
for tup in exptParameters['growth_value_tuples']}
phenotypeList = list(
set(list(zip(*exptParameters['condition_tuples']))[0]))
replicateList = sorted(
list(set(list(zip(*exptParameters['counts_file_list']))[1])))
phenotypeScoreDict = dict()
for (phenotype, condition1, condition2) in exptParameters['condition_tuples']:
for replicate in replicateList:
column1 = mergedCountsTable[(condition1, replicate)]
column2 = mergedCountsTable[(condition2, replicate)]
filtCols = filterLowCounts(pd.concat((column1, column2), axis=1, sort=True),
exptParameters['filter_type'], exptParameters['minimum_reads'])
score = computePhenotypeScore(filtCols[(condition1, replicate)], filtCols[(condition2, replicate)],
libraryTable[sublibColumn], growthValueDict[(
phenotype, replicate)],
exptParameters['pseudocount_behavior'], exptParameters['pseudocount'])
phenotypeScoreDict[(phenotype, replicate)] = score
if generatePlots != 'off':
tempDataDict = {'library': libraryTable[sublibColumn],
'counts': mergedCountsTable,
'phenotypes': pd.DataFrame(phenotypeScoreDict)}
printNow('-generating phenotype histograms and scatter plots')
for (phenotype, condition1, condition2) in exptParameters['condition_tuples']:
for replicate in replicateList:
screen_analysis.countsScatter(tempDataDict, condition1, replicate, condition2, replicate,
colorByPhenotype_condition=phenotype, colorByPhenotype_replicate=replicate)
screen_analysis.phenotypeHistogram(
tempDataDict, phenotype, replicate)
screen_analysis.sgRNAsPassingFilterHist(
tempDataDict, phenotype, replicate)
# scatterplot sgRNAs for all replicates, then average together and add columns to phenotype score table
if len(replicateList) > 1:
printNow('Averaging replicates')
for phenotype in phenotypeList:
repCols = pd.DataFrame({(phen, rep): col for (
phen, rep), col in phenotypeScoreDict.items() if phen == phenotype})
# average nan and real to nan; otherwise this could lead to data points with just one rep informing results
phenotypeScoreDict[(phenotype, 'ave_' + '_'.join(replicateList))
] = repCols.mean(axis=1, skipna=False)
phenotypeTable = pd.DataFrame(phenotypeScoreDict).sort_index(axis=1)
phenotypeTable.to_csv(outbase + '_phenotypetable.txt', sep='\t')
if len(replicateList) > 1 and generatePlots != 'off':
tempDataDict = {'library': libraryTable[sublibColumn],
'phenotypes': phenotypeTable}
printNow('-generating replicate phenotype histograms and scatter plots')
for phenotype, phengroup in phenotypeTable.groupby(level=0, axis=1):
for i, ((p, rep1), col1) in enumerate(phengroup.items()):
if rep1[:4] == 'ave_':
screen_analysis.phenotypeHistogram(
tempDataDict, phenotype, rep1)
for j, ((p, rep2), col2) in enumerate(phengroup.items()):
if rep2[:4] == 'ave_' or j <= i:
continue
else:
screen_analysis.phenotypeScatter(
tempDataDict, phenotype, rep1, phenotype, rep2)
# generate pseudogenes
negTable = phenotypeTable.loc[libraryTable[sublibColumn].loc[:,
'gene'] == 'negative_control', :]
if exptParameters['generate_pseudogene_dist'] != 'off' and len(exptParameters['analyses']) > 0:
print('Generating a pseudogene distribution from negative controls')
sys.stdout.flush()
pseudoTableList = []
pseudoLibTables = []
negValues = negTable.values
negColumns = negTable.columns
if exptParameters['generate_pseudogene_dist'].lower() == 'manual':
for pseudogene in range(exptParameters['num_pseudogenes']):
randIndices = np.random.randint(
0, len(negTable), exptParameters['pseudogene_size'])
pseudoTable = negValues[randIndices, :]
pseudoIndex = ['pseudo_%d_%d' % (pseudogene, i) for i in range(
exptParameters['pseudogene_size'])]
pseudoSeqs = ['seq_%d_%d' % (pseudogene, i) for i in range(
exptParameters['pseudogene_size'])] # so pseudogenes aren't treated as duplicates
pseudoTableList.append(pd.DataFrame(
pseudoTable, index=pseudoIndex, columns=negColumns))
pseudoLib = pd.DataFrame({'gene': ['pseudo_%d' % pseudogene]*exptParameters['pseudogene_size'],
'transcripts': ['na']*exptParameters['pseudogene_size'],
'sequence': pseudoSeqs}, index=pseudoIndex)
pseudoLibTables.append(pseudoLib)
elif exptParameters['generate_pseudogene_dist'].lower() == 'auto':
for pseudogene, (gene, group) in enumerate(libraryTable[sublibColumn].drop_duplicates(['gene', 'sequence']).groupby('gene')):
if gene == 'negative_control':
continue
for transcript, (transcriptName, transcriptGroup) in enumerate(group.groupby('transcripts')):
randIndices = np.random.randint(
0, len(negTable), len(transcriptGroup))
pseudoTable = negValues[randIndices, :]
pseudoIndex = ['pseudo_%d_%d_%d' % (
pseudogene, transcript, i) for i in range(len(transcriptGroup))]
pseudoSeqs = ['seq_%d_%d_%d' % (
pseudogene, transcript, i) for i in range(len(transcriptGroup))]
pseudoTableList.append(pd.DataFrame(
pseudoTable, index=pseudoIndex, columns=negColumns))
pseudoLib = pd.DataFrame({'gene': ['pseudo_%d' % pseudogene]*len(transcriptGroup),
'transcripts': ['pseudo_transcript_%d' % transcript]*len(transcriptGroup),
'sequence': pseudoSeqs}, index=pseudoIndex)
pseudoLibTables.append(pseudoLib)
else:
print('generate_pseudogene_dist parameter not recognized, defaulting to off')
phenotypeTable = pd.concat((phenotypeTable,
pd.concat(pseudoTableList, sort=True)))
libraryTableGeneAnalysis = pd.concat((libraryTable[sublibColumn],
pd.concat(pseudoLibTables, sort=True)))
else:
libraryTableGeneAnalysis = libraryTable[sublibColumn]
# compute gene scores for replicates, averaged reps, and pseudogenes
if len(exptParameters['analyses']) > 0:
print('Computing gene scores')
sys.stdout.flush()
phenotypeTable_deduplicated = phenotypeTable.loc[libraryTableGeneAnalysis.drop_duplicates([
'gene', 'sequence']).index]
if exptParameters['collapse_to_transcripts'] == True:
geneGroups = phenotypeTable_deduplicated.loc[libraryTableGeneAnalysis.loc[:, 'gene'] != 'negative_control', :].groupby(
[libraryTableGeneAnalysis['gene'], libraryTableGeneAnalysis['transcripts']])
else:
geneGroups = phenotypeTable_deduplicated.loc[libraryTableGeneAnalysis.loc[:, 'gene'] != 'negative_control', :].groupby(
libraryTableGeneAnalysis['gene'])
analysisTables = []
for analysis in exptParameters['analyses']:
print('--' + analysis)
sys.stdout.flush()
analysisTables.append(applyGeneScoreFunction(
geneGroups, negTable, analysis, exptParameters['analyses'][analysis]))
geneTable = pd.concat(analysisTables, axis=1, sort=True).reorder_levels(
[1, 2, 0], axis=1).sort_index(axis=1)
geneTable.to_csv(outbase + '_genetable.txt', sep='\t')
# collapse the gene-transcript indices into a single score for a gene by best MW p-value, where applicable
if exptParameters['collapse_to_transcripts'] == True and 'calculate_mw' in exptParameters['analyses']:
print('Collapsing transcript scores to gene scores')
sys.stdout.flush()
geneTableCollapsed = scoreGeneByBestTranscript(geneTable)
geneTableCollapsed.to_csv(
outbase + '_genetable_collapsed.txt', sep='\t')
# TODO: Fix the issues with Volcano Plots in the future...
""" if generatePlots != 'off':
if 'calculate_ave' in exptParameters['analyses'] and 'calculate_mw' in exptParameters['analyses']:
tempDataDict = {'library': libraryTable[sublibColumn],
'gene scores': geneTableCollapsed if exptParameters['collapse_to_transcripts'] else geneTable}
for (phenotype, replicate), gtable in tempDataDict['gene scores'].groupby(level=[0, 1], axis=1):
# just plot averaged reps where available
if len(replicateList) == 1 or replicate[:4] == 'ave_':
screen_analysis.volcanoPlot(
tempDataDict, phenotype, replicate, labelHits=False) """
print('Done!')
# given a gene table indexed by both gene and transcript, score genes by the best m-w p-value per phenotype/replicate
def scoreGeneByBestTranscript(geneTable):
geneTableTransGroups = geneTable.reorder_levels(
[2, 0, 1], axis=1)['Mann-Whitney p-value'].reset_index().groupby('gene')
bestTranscriptFrame = geneTableTransGroups.apply(getBestTranscript)
tupList = []
bestTransList = []
for tup, group in geneTable.groupby(level=list(range(2)), axis=1):
tupList.append(tup)
curFrame = geneTable.reindex(zip(
bestTranscriptFrame.index, bestTranscriptFrame[tup]),
axis=0).loc[:, tup]
bestTransList.append(curFrame.reset_index().set_index('gene'))
return pd.concat(bestTransList, axis=1, keys=tupList, sort=True)
def getBestTranscript(group):
# set the index to be transcripts and then get the index with the lowest p-value for each cell
return group.set_index('transcripts').drop(('gene', ''), axis=1).idxmin()
# return Series of counts from a counts file indexed by element id
def readCountsFile(countsFileName):
countsTable = pd.read_csv(
countsFileName, header=None, delimiter='\t', names=['id', 'counts'])
countsTable.index = countsTable['id']
return countsTable['counts']
# return DataFrame of library features indexed by element id
def readLibraryFile(libraryFastaFileName, elementTypeFunc, geneNameFunc, miscFuncList=None):
elementList = []
with open(libraryFastaFileName) as infile:
idLine = infile.readline()
while idLine != '':
seqLine = infile.readline()
if idLine[0] != '>' or seqLine == None:
raise ValueError('Error parsing fasta file')
elementList.append((idLine[1:].strip(), seqLine.strip()))
idLine = infile.readline()
elementIds, elementSeqs = zip(*elementList)
libraryTable = pd.DataFrame(np.array(elementSeqs), index=np.array(
elementIds), columns=['aligned_seq'], dtype='object')
libraryTable['element_type'] = elementTypeFunc(libraryTable)
libraryTable['gene_name'] = geneNameFunc(libraryTable)
if miscFuncList != None:
colList = [libraryTable]
for miscFunc in miscFuncList:
colList.append(miscFunc(libraryTable))
if len(colList) != 1:
libraryTable = pd.concat(colList, axis=1)
return libraryTable
# print all counts file paths, to assist with making an experiment table
def printCountsFilePaths(baseDirectoryPathList):
print('Make a tab-delimited file with the following columns:')
print('counts_file\texperiment\tcondition\treplicate_id')
print('and the following list in the counts_file column:')
for basePath in baseDirectoryPathList:
for root, dirs, filenames in os.walk(basePath):
for filename in fnmatch.filter(filenames, '*.counts'):
print(os.path.join(root, filename))
def mergeCountsForExperiments(experimentFileName, libraryTable):
exptTable = pd.read_csv(experimentFileName, delimiter='\t')
print(exptTable)
# load in all counts independently
countsCols = []
for countsFile in exptTable['counts_file']:
countsCols.append(readCountsFile(countsFile))
countsTable = pd.concat(countsCols, axis=1, keys=exptTable['counts_file']).align(
libraryTable, axis=0)[0]
# nan values are 0 values, will use nan to filter out elements later
countsTable = countsTable.fillna(value=0)
# print countsTable.head()
# convert counts columns to experiments, summing when reads across multiple lanes
exptTuples = [(exptTable.loc[row, 'experiment'], exptTable.loc[row, 'condition'],
exptTable.loc[row, 'replicate_id']) for row in exptTable.index]
exptTuplesToRuns = dict()
for i, tup in enumerate(exptTuples):
if tup not in exptTuplesToRuns:
exptTuplesToRuns[tup] = []
exptTuplesToRuns[tup].append(exptTable.loc[i, 'counts_file'])
# print exptTuplesToRuns
exptColumns = []
for tup in sorted(exptTuplesToRuns.keys()):
if len(exptTuplesToRuns[tup]) == 1:
exptColumns.append(countsTable[exptTuplesToRuns[tup][0]])
else:
column = countsTable[exptTuplesToRuns[tup][0]]
for i in range(1, len(exptTuplesToRuns[tup])):
column += countsTable[exptTuplesToRuns[tup][i]]
exptColumns.append(column)
# print len(exptColumns), exptColumns[-1]
exptsTable = pd.concat(exptColumns, axis=1, keys=sorted(
exptTuplesToRuns.keys()), sort=True)
exptsTable.columns = pd.MultiIndex.from_tuples(
sorted(exptTuplesToRuns.keys()))
# print exptsTable
#mergedTable = pd.concat([libraryTable,countsTable,exptsTable],axis=1, keys = ['library_properties','raw_counts', 'merged_experiments'])
return countsTable, exptsTable
# filter out reads if /all/ reads for an expt accross replicates/conditions < min_reads
def filterCountsPerExperiment(min_reads, exptsTable, libraryTable):
experimentGroups = []
exptTuples = exptsTable.columns
exptSet = set([tup[0] for tup in exptTuples])
for expt in exptSet:
exptDf = exptsTable[[tup for tup in exptTuples if tup[0] == expt]]
exptDfUnderMin = (exptDf < min_reads).all(axis=1)
exptDfFiltered = exptDf.align(
exptDfUnderMin[exptDfUnderMin == False], axis=0, join='right')[0]
experimentGroups.append(exptDfFiltered)
print(expt, len(exptDfUnderMin[exptDfUnderMin == True]))
resultTable = pd.concat(experimentGroups, axis=1,
sort=True).align(libraryTable, axis=0)[0]
return resultTable
# more flexible read filtering
# keep row if either both/all columns are above threshold, or if either/any column is
# in other words, mask if any column is below threshold or only if all columns are below
def filterLowCounts(countsColumns, filterType, filterThreshold):
if filterType == 'both' or filterType == 'all':
failFilterColumn = countsColumns.apply(
lambda row: min(row) < filterThreshold, axis=1)
elif filterType == 'either' or filterType == 'any':
failFilterColumn = countsColumns.apply(
lambda row: max(row) < filterThreshold, axis=1)
else:
raise ValueError('filter type not recognized or not implemented')
resultTable = countsColumns.copy()
resultTable.loc[failFilterColumn, :] = np.nan
return resultTable
# compute phenotype scores for any given comparison of two conditions
def computePhenotypeScore(counts1, counts2, libraryTable, growthValue, pseudocountBehavior, pseudocountValue, normToNegs=True):
combinedCounts = pd.concat([counts1, counts2], axis=1, sort=True)
# pseudocount
if pseudocountBehavior == 'default' or pseudocountBehavior == 'zeros only':
def defaultBehavior(row): return row if min(
row) != 0 else row + pseudocountValue
combinedCountsPseudo = combinedCounts.apply(defaultBehavior, axis=1)
elif pseudocountBehavior == 'all values':
combinedCountsPseudo = combinedCounts.apply(
lambda row: row + pseudocountValue, axis=1)
elif pseudocountBehavior == 'filter out':
combinedCountsPseudo = combinedCounts.copy()
zeroRows = combinedCounts.apply(lambda row: min(row) <= 0, axis=1)
combinedCountsPseudo.loc[zeroRows, :] = np.nan
else:
raise ValueError(
'Pseudocount behavior not recognized or not implemented')
totalCounts = combinedCountsPseudo.sum()
countsRatio = float(totalCounts[0])/totalCounts[1]
# compute neg control log2 enrichment
if normToNegs == True:
negCounts = combinedCountsPseudo.align(
libraryTable[libraryTable['gene'] == 'negative_control'], axis=0, join='inner')[0]
# print negCounts
else:
negCounts = combinedCountsPseudo
neglog2e = negCounts.apply(
calcLog2e, countsRatio=countsRatio, growthValue=1, wtLog2E=0, axis=1).median()
# print neglog2e
# compute phenotype scores
scores = combinedCountsPseudo.apply(
calcLog2e, countsRatio=countsRatio, growthValue=growthValue, wtLog2E=neglog2e, axis=1)
return scores
def calcLog2e(row, countsRatio, growthValue, wtLog2E):
return (np.log2(countsRatio*row[1]/row[0]) - wtLog2E) / growthValue
# average replicate phenotype scores
def averagePhenotypeScores(scoreTable):
exptTuples = scoreTable.columns
exptsToReplicates = dict()
for tup in exptTuples:
if (tup[0], tup[1]) not in exptsToReplicates:
exptsToReplicates[(tup[0], tup[1])] = set()
exptsToReplicates[(tup[0], tup[1])].add(tup[2])
averagedColumns = []
labels = []
for expt in exptsToReplicates:
exptDf = scoreTable[[(expt[0], expt[1], rep_id)
for rep_id in exptsToReplicates[expt]]]
averagedColumns.append(exptDf.mean(axis=1))
labels.append((expt[0], expt[1], 'ave_' +
'_'.join(exptsToReplicates[expt])))
resultTable = pd.concat(averagedColumns, axis=1,
keys=labels, sort=True).align(scoreTable, axis=0)[0]
resultTable.columns = pd.MultiIndex.from_tuples(labels)
return resultTable
# apply gene scoring functions to pre-grouped tables of phenotypes
def applyGeneScoreFunction(groupedPhenotypeTable, negativeTable, analysis, analysisParamList):
if analysis == 'calculate_ave':
numToAverage = analysisParamList[0]
if numToAverage <= 0:
means = groupedPhenotypeTable.aggregate(np.mean)
counts = groupedPhenotypeTable.count()
result = pd.concat([means, counts], axis=1, keys=[
'average of all phenotypes', 'average of all phenotypes_sgRNAcount'], sort=True)
else:
means = groupedPhenotypeTable.apply(
lambda x: averageBestN(x, numToAverage))
counts = groupedPhenotypeTable.count()
result = pd.concat([means, counts], axis=1, keys=[
'average phenotype of strongest %d' % numToAverage, 'sgRNA count_avg'], sort=True)
elif analysis == 'calculate_mw':
pvals = groupedPhenotypeTable.apply(
lambda x: applyMW(x, negativeTable))
counts = groupedPhenotypeTable.count()
result = pd.concat([pvals, counts], axis=1, keys=[
'Mann-Whitney p-value', 'sgRNA count_MW'], sort=True)
elif analysis == 'calculate_nth':
nth = analysisParamList[0]
pvals = groupedPhenotypeTable.aggregate(lambda x: sorted(
x, key=abs, reverse=True)[nth-1] if nth <= len(x) else np.nan)
counts = groupedPhenotypeTable.count()
result = pd.concat([pvals, counts], axis=1, keys=[
'%dth best score' % nth, 'sgRNA count_nth best'], sort=True)
else:
raise ValueError(
'Analysis %s not recognized or not implemented' % analysis)
return result
def averageBestN(group, numToAverage):
return group.apply(lambda column: np.mean(sorted(column.dropna(), key=abs, reverse=True)[:numToAverage]) if len(column.dropna()) > 0 else np.nan)
def applyMW(group, negativeTable):
sp_version = [int(v) for v in sp.__version__.split('.')]
if sp_version[0] >= 1 and sp_version[1] >= 6: #introduction of "exact" p-value calculation which can be prohibitively slow and does not match original behavior
return group.apply(lambda column: stats.mannwhitneyu(column.dropna().values, negativeTable[column.name].dropna().values, alternative='two-sided', method='asymptotic')[1] \
if len(column.dropna()) > 0 else np.nan)
elif (sp_version[0] == 0 and sp_version[1] >= 17) or sp_version[0] >= 1: # implementation of the "alternative flag"
return group.apply(lambda column: stats.mannwhitneyu(column.dropna().values, negativeTable[column.name].dropna().values, alternative='two-sided')[1] \
if len(column.dropna()) > 0 else np.nan)
else: # pre v0.17 stats.mannwhitneyu is one-tailed!!
return group.apply(lambda column: stats.mannwhitneyu(column.dropna().values, negativeTable[column.name].dropna().values)[1] * 2 if len(column.dropna()) > 0 else np.nan)
# parse a tab-delimited file with column headers: experiment, replicate_id, G_value, K_value (calculated with martin's parse_growthdata.py)
def parseGKFile(gkFileName):
gkdict = dict()
with open(gkFileName, 'rU') as infile:
for line in infile:
if line.split('\t')[0] == 'experiment':
continue
else:
linesplit = line.strip().split('\t')
gkdict[(linesplit[0], linesplit[1])] = (
float(linesplit[2]), float(linesplit[3]))
return gkdict