def printMissingSequences(missingSequences=None,
databaseVersion=None,
outputDirectory=None,
fileVersion='1.0',
verbose=False):
outputFileNameShort = databaseVersion + '_Missing_Reference_Alleles.txt'
outputFileNameFull = join(outputDirectory, outputFileNameShort)
if (verbose):
print('Writing a list of ' + str(len(missingSequences)) +
' missing allele sequences to:' + str(outputFileNameFull))
outputFile = open(outputFileNameFull, 'w')
outputFile.write('# filename: ' + str(outputFileNameShort) + '\n')
outputFile.write('# date: ' + datetime.today().strftime('%Y-%m-%d') + '\n')
outputFile.write('# version: ' + str(fileVersion) + '\n')
outputFile.write('# author: ' +
str('Ben Matern <*****@*****.**>') + '\n')
alleleClusters = clusterSequences(alleleSequences=missingSequences,
verbose=verbose)
for locus in sorted(alleleClusters.keys()):
for alleleGroup in sorted(alleleClusters[locus].keys()):
for allele in alleleClusters[locus][alleleGroup]:
outputFile.write(str(allele.alleleName) + '\n')
outputFile.close()
def printSequenceCountsPerLocus(alleleSequences=None,
outputFilename=None,
verbose=None,
imgtReleaseVersion=None,
delimiter='\t'):
if (verbose):
print('Creating sequence counts per locus:' + str(outputFilename))
outputFile = open(outputFilename, 'w')
outputFile.write('Locus' + delimiter + imgtReleaseVersion +
' Reference Count' + '\n')
# Loop sequences:
alleleClusters = clusterSequences(alleleSequences=alleleSequences,
verbose=verbose)
for locus in sorted(alleleClusters.keys()):
# print('Finding reference for locus ' + str(locus))
seqCount = 0
for alleleGroup in sorted(alleleClusters[locus].keys()):
seqCount += len(alleleClusters[locus][alleleGroup])
outputFile.write(locus + delimiter + str(seqCount) + '\n')
# Write TOtal
outputFile.write('Total' + delimiter + str(len(alleleSequences)) + '\n')
outputFile.close()
def printSequenceList(alleleSequences=None,
databaseVersion=None,
outputDirectory=None,
fileVersion='1.0',
verbose=False,
alleleDescriptionLookup=None):
outputFileNameShort = databaseVersion + '_Reference_Alleles.txt'
outputFileNameFull = join(outputDirectory, outputFileNameShort)
if (verbose):
print('Writing a list of ' + str(len(alleleSequences)) +
' allele sequences to:' + str(outputFileNameFull))
outputFile = open(outputFileNameFull, 'w')
outputFile.write('# filename: ' + str(outputFileNameShort) + '\n')
outputFile.write('# date: ' + datetime.today().strftime('%Y-%m-%d') + '\n')
outputFile.write('# version: ' + str(fileVersion) + '\n')
outputFile.write('# author: ' +
str('Ben Matern <*****@*****.**>') + '\n')
outputFile.write('IPD-IMGT/HLA Database ' + str(databaseVersion) +
' Accession Number\tLocus\tIPD-IMGT/HLA Database ' +
str(databaseVersion) + ' Allele Name\tDescription\n')
locusReferences = getLocusReferences()
#Cluster to sort them
alleleClusters = clusterSequences(alleleSequences=alleleSequences,
verbose=verbose)
for locus in sorted(alleleClusters.keys()):
#print('Finding reference for locus ' + str(locus))
for alleleGroup in sorted(alleleClusters[locus].keys()):
for allele in alleleClusters[locus][alleleGroup]:
currentLocus, nomenclatureFields = allele.alleleName.split('*')
nomenclatureTokens = nomenclatureFields.split(':')
currentGroup = str(nomenclatureTokens[0])
allele.description = ''
# Is it a locus reference?
for locusReference in list(set(locusReferences)):
if (allele.alleleName in locusReference
or locusReference in allele.alleleName):
allele.description = currentLocus + ' Locus Reference;'
# If we already have a description (serotype or DP references)
if allele.alleleName in alleleDescriptionLookup.keys():
allele.description += alleleDescriptionLookup[
allele.alleleName]
else:
# Otherwise it's a group reference.
allele.description += currentLocus.replace(
'HLA-', '') + '*' + currentGroup + ' Reference'
outputFile.write(
str(allele.accessionNumber) + '\t' + currentLocus + '\t' +
str(allele.alleleName) + '\t' + str(allele.description) +
'\n')
outputFile.close()
def printSequences(alleleSequences=None, outputFilename=None, verbose=False):
if (verbose):
print('Writing ' + str(len(alleleSequences)) +
' allele sequences to:' + str(outputFilename))
outputFile = open(outputFilename, 'w')
alleleClusters = clusterSequences(alleleSequences=alleleSequences,
verbose=verbose)
for locus in sorted(alleleClusters.keys()):
# print('Finding reference for locus ' + str(locus))
for alleleGroup in sorted(alleleClusters[locus].keys()):
for alleleSequence in alleleClusters[locus][alleleGroup]:
outputFile.write('>' + str(alleleSequence.alleleName) + '\n')
outputFile.write(str(alleleSequence.getSequence()) + '\n')
outputFile.close()
def printSequenceDetails(alleleSequences=None,
outputFilename=None,
verbose=False,
delimiter='\t',
imgtReleaseVersion=None):
if (verbose):
print('Creating Sequence Details file:' + str(outputFilename))
outputFile = open(outputFilename, 'w')
outputFile.write(imgtReleaseVersion + ' Allele Name' + delimiter +
imgtReleaseVersion + ' Sequence Length' + delimiter +
imgtReleaseVersion + ' 5\'UTR Length' + delimiter +
imgtReleaseVersion + ' 3\'UTR Length' + delimiter +
imgtReleaseVersion + ' CWD Status' + '\n')
# Loop sequences:
alleleClusters = clusterSequences(alleleSequences=alleleSequences,
verbose=verbose)
for locus in sorted(alleleClusters.keys()):
# print('Finding reference for locus ' + str(locus))
for alleleGroup in sorted(alleleClusters[locus].keys()):
for alleleSequence in alleleClusters[locus][alleleGroup]:
# TODO: This will break if the feature is missing. Only running on full-len for now.
# Placeholder fix for missing 5 and 3 UTRs.
if ('5UTR' not in alleleSequence.featureSequences.keys()):
utr5Sequence = ''
else:
utr5Sequence = alleleSequence.featureSequences['5UTR']
if ('3UTR' not in alleleSequence.featureSequences.keys()):
utr3Sequence = ''
else:
utr3Sequence = alleleSequence.featureSequences['3UTR']
outputFile.write(alleleSequence.alleleName + delimiter +
str(len(alleleSequence.getSequence())) +
delimiter + str(len(utr5Sequence)) +
delimiter + str(len(utr3Sequence)) +
delimiter + str(alleleSequence.cwdStatus) +
'\n')
outputFile.close()
# TODO: The database version from the XML file may be slightly different than the provided release number, due to minor versioning.
# I am naming files based on the "0" version but there might be 3.42.1 for example.
# Not completely accurate but its more consistent this way. May cause confusion.
if (databaseVersion != args.release):
print(
'Warning! the latest IPD-IMGT/HLA xml file shows a different (newer?) release date ('
+ str(databaseVersion) + ') than the provided release version (' +
str(args.release) + ')')
if (args.supplementary):
printSequences(alleleSequences=alleleSequences,
outputFilename=join(
supplementalFileDirectory,
str(args.release) + '_FullLengthSequences.fasta'),
verbose=verbose)
alleleSequenceClusters = clusterSequences(alleleSequences=alleleSequences,
verbose=verbose)
newReferenceSequences, missingSequences, alleleDescriptionLookup = createReferenceSequences(
clusteredFullLenAlleleSequences=alleleSequenceClusters,
verbose=verbose,
imgtReleaseVersion=args.release)
printSequences(alleleSequences=newReferenceSequences,
outputFilename=join(
outputDirectory,
str(args.release) + '_ReferenceSequences.fasta'),
verbose=verbose)
printSequenceList(alleleSequences=newReferenceSequences,
databaseVersion=args.release,
outputDirectory=outputDirectory,
verbose=verbose,
fileVersion=args.version,
alleleDescriptionLookup=alleleDescriptionLookup)