def runDistributed():
import _distributed
import dask
scheduler = _distributed.open()
delayedCalls = []
for taxId in allSpeciesSource():
if not getSpeciesProperty(taxId, "ENc-prime")[0] is None:
continue
print(taxId)
call = dask.delayed(annotateENcPrime)(taxId)
delayedCalls.append(call)
print("Starting %d calls..." % len(delayedCalls))
futures = scheduler.compute(
delayedCalls
) # submit all delayed calculations; obtain futures immediately
try:
_distributed.progress(futures) # wait for all calculations to complete
except Exception as e:
print(E)
print("\n")
print("Waiting for all tasks to complete...")
_distributed.wait(futures)
results = {}
errorsCount = 0
newValuesCount = 0
oldValuesCount = 0
for f in futures:
try:
(taxId, ENc, ENc_prime, isFreshValue) = scheduler.gather(f)
results[taxId] = (ENc, ENc_prime)
if isFreshValue:
newValuesCount += 1
else:
oldValuesCount += 1
except Exception as e:
print(e)
errorsCount += 1
print("Finished %d species with %d errors" % (len(results), errorsCount))
print("{} new values; {} old values".format(newValuesCount,
oldValuesCount))
return results
def calcFastaProfiles(fastaInput):
import dask
delayedCalls = []
for (seqId, seq) in fastaSequencesSource(fastaInput):
#if random.randint(0, 100) > 0:
# continue
call = dask.delayed(calculateNativeProfileForSequence)(seqId, seq, 31,
1)
delayedCalls.append(call)
print("Starting %d calls..." % len(delayedCalls))
futures = scheduler.compute(
delayedCalls
) # submit all delayed calculations; obtain futures immediately
try:
_distributed.progress(futures) # wait for all calculations to complete
except Exception as e:
print(E)
print("\n")
print("Waiting for all tasks to complete...")
_distributed.wait(futures)
errorsCount = 0
results = []
for f in futures:
try:
(seqId, profile) = scheduler.gather(f)
results.append((seqId, profile))
except Exception as e:
print(e)
errorsCount += 1
with open("{}.profiles.csv".format(fastaInput), "wb") as csvfile:
csvout = csv.writer(csvfile)
for (seqId, profile) in results:
csvout.writerow([seqId] + profile)
if errorsCount:
print("==" * 20)
print("Finished with %d errors!" % errorsCount)
print("==" * 20)
def runDistributed(args):
import _distributed
import dask
scheduler = _distributed.open()
results = {}
taxids = []
delayedCalls = []
for taxid in args.taxid:
call = dask.delayed(calcProfilesForSpeciesX)(taxid, args)
delayedCalls.append(call)
taxids.append(taxid)
futures = scheduler.compute(
delayedCalls
) # submit all delayed calculations; obtain futures immediately
try:
_distributed.progress(futures) # wait for all calculations to complete
except Exception as e:
print(E)
print("\n")
print("Waiting for all tasks to complete...")
_distributed.wait(futures)
results = {}
errorsCount = 0
for taxid, f in zip(taxids, futures):
try:
r = scheduler.gather(f)
returnedTaxId = r[0]
assert (taxid == returnedTaxId)
results[taxid] = r
except Exception as e:
print(e)
results[taxid] = None
errorsCount += 1
print("Finished with %d errors" % errorsCount)
return results
def runDistributed():
import _distributed
import dask
scheduler = _distributed.open()
results = {}
#taxids = []
delayedCalls = []
fractionSize = 20
for taxId in allSpeciesSource():
if randint(0, 20) > 0:
continue
if not getSpeciesProperty(taxId, 'paired-mRNA-fraction')[0] is None:
continue
size = countSpeciesCDS(taxId)
numFractions = size / fractionSize
for i in range(numFractions):
call = dask.delayed(calcNativePairedFraction)(taxId, i,
numFractions)
delayedCalls.append(call)
#taxids.append(taxId)
print("Starting %d calls..." % len(delayedCalls))
futures = scheduler.compute(
delayedCalls
) # submit all delayed calculations; obtain futures immediately
try:
_distributed.progress(futures) # wait for all calculations to complete
except Exception as e:
print(E)
print("\n")
print("Waiting for all tasks to complete...")
_distributed.wait(futures)
results = {}
errorsCount = 0
for f in futures:
try:
(taxId, fraction, cdsCount, countPairedNucleotides,
countTotalNucleotides) = scheduler.gather(f)
current = None
if taxId in results:
current = results[taxId]
else:
current = (0, 0, 0, set())
current = (current[0] + cdsCount,
current[1] + countPairedNucleotides,
current[2] + countTotalNucleotides,
current[3].union(set((fraction, ))))
results[taxId] = current
except Exception as e:
print(e)
errorsCount += 1
for taxId, result in results.items():
if len(result[3]) != max(result[3]) + 1:
#raise Exception("Found invalid number of items for taxId=%d" % taxId)
print("Found invalid number of items for taxId=%d" % taxId)
continue
fraction = float(result[1]) / result[2]
setSpeciesProperty(taxId,
"paired-mRNA-fraction",
"%.4g" % fraction,
"computed (v3)",
overwrite=False)
print("TaxId: %d\t\tFraction: %.4g" % (taxId, fraction))
print("Finished %d species with %d errors" % (len(results), errorsCount))
return results
def speciesStatisticsAndValidityReport(args):
import _distributed
speciesDf = pd.DataFrame({
'TaxId': pd.Series([], dtype='int'), # Species TaxId
'Species': pd.Series([], dtype='str'), # Species binomial name
'Nickname': pd.Series([], dtype='str'),
'Domain': pd.Categorical([]), # Bacteria, Eukaryota, Archaea
'Phylum': pd.Categorical([]), # Phylum name (string)
'NumCDSs': pd.Series([], dtype='int'), # CDS count for this species
'NumCDSsInProfile':
pd.Series([], dtype='int'
), # Num seqs with 20 shuffled profiles for this species
'AnnotatedNumCDSs': pd.Series([], dtype='int'), #
'CDSDifference': pd.Series([], dtype='float'), #
'NumNativeSeqs': pd.Series([], dtype='int'), #
'GCContentInCDS': pd.Series([], dtype='float'), #
'AnnotatedGCContent': pd.Series([], dtype='float'), #
'RowType': pd.Categorical([]), # Species count or total
'Warnings': pd.Series([], dtype='str'), #
'CDSWarnings': pd.Series([], dtype='int'), #
'CDSWarnings_': pd.Series([], dtype='str'), #
'FirstAA': pd.Series([], dtype='str'), #
'LastAA': pd.Series([], dtype='str') #
})
scheduler = _distributed.open()
results = {}
delayedCalls_native = []
shuffledCounts = {}
delayedCalls_shuffledProfiles = []
for taxId in allSpeciesSource():
if taxId in speciesToExclude:
continue # always exclude species from the blacklist
if args.taxid and taxId not in args.taxid:
continue # if a whitelist is specified, skip other species
warnings = []
## DEBUG ONLY ### DEBUG ONLY ### DEBUG ONLY ### DEBUG ONLY ### DEBUG ONLY ### DEBUG ONLY ##
#if randint(0, 20) > 0:
# continue
## DEBUG ONLY ### DEBUG ONLY ### DEBUG ONLY ### DEBUG ONLY ### DEBUG ONLY ### DEBUG ONLY ##
cdsCountInRedis = countSpeciesCDS(taxId)
#cdsCountProfiles = countx(taxId, (310, 10, "begin", 0), 102, 11)
annotatedProteinCount = getSpeciesProperty(taxId, 'protein-count')[0]
annotatedGCContent = getSpeciesProperty(taxId, 'gc-content')[0]
proteinDifference = None
if not annotatedProteinCount is None:
proteinDifference = (1.0 - float(cdsCountInRedis) /
float(annotatedProteinCount)) * 100.0
if abs(proteinDifference) > 9.9:
warnings.append("CDS_count")
else:
warnings.append("No_CDS_count")
# Determine phylum
lineage = ncbiTaxa.get_lineage(taxId)
names = ncbiTaxa.get_taxid_translator(lineage)
ranks = ncbiTaxa.get_rank(lineage)
# Determine kingdom/domain
domain = ""
kingdomTaxId = [
t for t, rank in ranks.items() if rank == 'superkingdom'
]
if not kingdomTaxId:
kingdomTaxId = [
t for t, rank in ranks.items() if rank == 'kingdom'
]
domain = names[kingdomTaxId[0]]
phylumName = ""
# Determine phylum
phylumTaxId = [t for t, rank in ranks.items() if rank == 'phylum']
if phylumTaxId:
phylumName = names[phylumTaxId[0]]
speciesDf = speciesDf.append(
pd.DataFrame({
'TaxId':
pd.Series([taxId], dtype='int'), # Species TaxId
'Species':
pd.Series([getSpeciesName(taxId)], dtype='str'),
'Nickname':
pd.Series([shortNames[taxId]], dtype='str'),
'Domain':
pd.Categorical([domain]), # Bacteria, Eukaryota, Archaea
'Phylum':
pd.Categorical([phylumName]), # Phylum name (string)
'NumCDSs':
pd.Series([cdsCountInRedis],
dtype='int'), # CDS count for this species
'NumCDSsInProfile':
pd.Series([0],
dtype='int'), # Num seqs with 20 shuffled profiles
'AnnotatedNumCDSs':
pd.Series([
0
if annotatedProteinCount is None else annotatedProteinCount
],
dtype='int'), #
'CDSDifference':
pd.Series([proteinDifference], dtype='float'), #
'NumNativeSeqs':
pd.Series([0], dtype='int'), #
'GCContentInCDS':
pd.Series([0.0], dtype='float'), #
'AnnotatedGCContent':
pd.Series([annotatedGCContent], dtype='float'), #
'RowType':
pd.Categorical(["species"]), # Species count or total
'Warnings':
pd.Series([", ".join(warnings)], dtype='str'), #
'CDSWarnings':
pd.Series([0], dtype='int'),
'CDSWarnings_':
pd.Series([""], dtype='str'),
'FirstAA':
pd.Series([""], dtype='str'),
'LastAA':
pd.Series([""], dtype='str'),
'Source':
pd.Series([""], dtype='str')
}))
fractionSize = 1000 # How many sequences (roughly) to process in each task
numFractions = cdsCountInRedis / fractionSize
if numFractions == 0: numFractions = 1
for i in range(numFractions):
# DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #
#if i%100!=5: continue
# DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #### DEBUG ONLY #
call = dask.delayed(calcNativeSequencesStatistics)(taxId, i,
numFractions)
delayedCalls_native.append(call)
call = dask.delayed(countShuffledProfiles)(taxId,
(310, 10, "begin", 0), 102,
11)
delayedCalls_shuffledProfiles.append(call)
speciesDf.set_index('TaxId', inplace=True)
print("Starting {} calls...".format(
len(delayedCalls_native) + len(delayedCalls_shuffledProfiles)))
futures = scheduler.compute(
delayedCalls_native + delayedCalls_shuffledProfiles
) # submit all delayed calculations; obtain futures immediately
try:
_distributed.progress(futures) # wait for all calculations to complete
except Exception as e:
print(E)
print("\n")
print("Waiting for all tasks to complete...")
_distributed.wait(futures)
results = {}
errorsCount = 0
for f in futures:
try:
ret = scheduler.gather(f)
if (len(ret) == 9):
(taxId, fraction, cdsCount, gcCounts, totalCounts, cdsWarnings,
warnings, firstAA, lastAA) = ret
current = None
if taxId in results:
current = results[taxId]
else:
current = (0, 0, 0, 0, Counter(), Counter(), Counter())
current = (current[0] + cdsCount, current[1] + gcCounts,
current[2] + totalCounts, current[3] + cdsWarnings,
current[4] + warnings, current[5] + firstAA,
current[6] + lastAA)
results[taxId] = current
elif (len(ret) == 2):
(taxId, numShuffledSeqs) = ret
shuffledCounts[taxId] = numShuffledSeqs
else:
assert (False)
except Exception as e:
print(e)
errorsCount += 1
for taxId, result in results.items():
(numNativeSeqs, gcCounts, totalCounts, cdsWarnings, warnings, firstAA,
lastAA) = result
speciesDf.at[taxId, 'NumNativeSeqs'] = numNativeSeqs
speciesDf.at[taxId, 'GCContentInCDS'] = round(
float(gcCounts) / float(totalCounts) * 100.0, 1)
speciesDf.at[taxId, 'CDSWarnings'] = cdsWarnings
speciesDf.at[taxId, 'CDSWarnings_'] = summarizeCounter(warnings)
speciesDf.at[taxId, 'FirstAA'] = summarizeCounter(firstAA)
speciesDf.at[taxId, 'LastAA'] = summarizeCounter(lastAA)
#if numNativeSeqs < species.at[taxId, 'NumCDSs']:
# pass
for taxId, result in shuffledCounts.items():
speciesDf.at[taxId, 'NumCDSsInProfile'] = result
speciesDf = speciesDf.sort_values(by=['Domain', 'Species']) # sort rows
speciesDf.to_html('species_report.html',
float_format='{0:.1f}'.format,
columns=[
'Species', 'Nickname', 'NumCDSs', 'NumCDSsInProfile',
'AnnotatedNumCDSs', 'CDSDifference', 'NumNativeSeqs',
'GCContentInCDS', 'AnnotatedGCContent', 'Phylum',
'Domain', 'Warnings', 'CDSWarnings', 'CDSWarnings_',
'FirstAA', 'LastAA'
])
with open("species_report_simple.rst", "w") as f:
f.write(
speciesDf.drop([
'RowType', 'Warnings', 'CDSWarnings', 'CDSWarnings_',
'FirstAA', 'LastAA', 'CDSDifference'
],
axis=1).pipe(tabulate,
headers='keys',
tablefmt='rst'))
speciesDf.to_html('species_report_simple.html',
float_format='{0:.1f}'.format,
columns=[
'Species', 'Nickname', 'NumCDSs', 'NumCDSsInProfile',
'AnnotatedNumCDSs', 'CDSDifference', 'NumNativeSeqs',
'GCContentInCDS', 'AnnotatedGCContent', 'Phylum',
'Domain'
])
speciesDf.to_excel('species_report.xlsx', sheet_name='Species summary')
