def runPairWiseDiffs(self, fastaFileNames):
print 'Calculating pairwise diffenrences...',
# Read in fasta sequences into a dictionary:
completeSets = {}
for fastaFileName in fastaFileNames:
baseName = os.path.splitext(os.path.basename(fastaFileName))[0]
#baseName = os.path.basename(fastaFileName).split(".")[0]
completeSets[baseName] = {}
fastaFile = open(fastaFileName, 'r')
fastaIterator = Fasta.Iterator(fastaFile,
parser=Fasta.RecordParser())
for fastaRecord in fastaIterator:
newName = safeName(copy.copy(fastaRecord.title))
#completeSets[baseName][fastaRecord.title.strip()] = fastaRecord.sequence
completeSets[baseName][newName] = fastaRecord.sequence
fastaFile.close()
# Load existing alignment matrix
alignmentMatrices = {}
for fastaFileBaseName in completeSets.keys():
if not alignmentMatrices.has_key(fastaFileBaseName):
alignmentMatrices[fastaFileBaseName] = {}
alignmentMatrixFileName = os.path.join(
self.options.statsdir, fastaFileBaseName + "_matrix.pickle")
if os.path.exists(alignmentMatrixFileName) and os.path.getsize(
alignmentMatrixFileName) > 0:
alignmentMatrixFile = open(alignmentMatrixFileName, 'r')
alignmentMatrices[fastaFileBaseName] = pickle.load(
alignmentMatrixFile)
alignmentMatrixFile.close()
# Add any new alignments to alignment matrix (and save to them to file)
self.updateAlignmentMatrix(alignmentMatrices, completeSets)
print 'done'
def fixAndMoveInput(self, files, outputDir=None):
if not outputDir:
outputDir = self.options.datadir
allowedLetters = IUPAC.IUPACAmbiguousDNA(
).letters + IUPAC.IUPACAmbiguousDNA().letters.lower()
sequenceCount = 0
inputFileList = []
sequenceNameMap = {}
for inputFileName in files:
if not os.path.exists(inputFileName):
raise AnalysisTerminated(
1, " Input filename %s does not exist!" % inputFileName)
# print " Input filename %s does not exist!" % inputFileName
# sys.exit(1)
if self.options.inputformat == 'nexus':
nex = Nexus.Nexus(inputFileName)
fileContent = ''
for name, seq in nex.matrix.items():
fileContent += ">%s\n%s\n" % (name, str(seq))
elif self.options.inputformat == 'fasta':
fileContent = readFile(inputFileName)
else:
raise AnalysisTerminated(
1, "The supported input formats are 'fasta' and 'nexus'")
# print "The supported input formats are 'fasta' and 'nexus'"
# sys.exit()
fileContent = re.sub(r'\r+', '\n', fileContent)
tmpOutputFileName = os.path.join(
outputDir, "%s.tmp" % os.path.split(inputFileName)[-1])
writeFile(tmpOutputFileName, fileContent)
usedIDs = {}
inputFile = open(tmpOutputFileName, 'r')
fastaIterator = Fasta.Iterator(inputFile,
parser=Fasta.RecordParser())
outputFileBaseName = os.path.split(inputFileName)[-1]
newOutputFileBaseName = re.sub(r'[^0-9a-zA-Z.]+', '',
outputFileBaseName)
if re.match(r'\d', newOutputFileBaseName):
newOutputFileBaseName = 'n' + newOutputFileBaseName
outputFileName = os.path.join(outputDir, newOutputFileBaseName)
baseName = os.path.splitext(os.path.basename(outputFileName))[0]
sequenceNameMap[baseName] = {}
inputFileList.append(outputFileName)
outputFile = open(outputFileName, 'w')
for fastaRecord in fastaIterator:
sequenceCount += 1
origName = fastaRecord.title
fastaRecord.title = safeName(fastaRecord.title)
# Make sure ids are unique:
if usedIDs.has_key(
fastaRecord.title.lower()
): # we use lower to make sure they don't just differ in case.
i = 1
while usedIDs.has_key("%s_%d" % (fastaRecord.title, i)):
i += 1
fastaRecord.title = "%s_%d" % (fastaRecord.title, i)
usedIDs[fastaRecord.title.lower()] = True
sequenceNameMap[baseName][fastaRecord.title] = origName
# Strip sequence of gap chars:
#fastaRecord.sequence = fastaRecord.sequence.replace('-', '')
fastaRecord.sequence = fastaRecord.sequence.replace('~', '')
fastaRecord.sequence = fastaRecord.sequence.replace('.', '')
# if allowedLetters is None:
# if len(re.findall(IUPAC.IUPACAmbiguousDNA().letters, fastaRecord.sequence)) / len(fastaRecord.sequence) > 0.5:
# allowedLetters = IUPAC.IUPACAmbiguousDNA().letters
# wildcard = 'N'
# else:
# allowedLetters = ExtendedIUPACProtein().letters
# wildcard = 'X'
# fastaRecord.sequence = re.sub('[^%s-]' % allowedLetters, wildcard, fastaRecord.sequence)
# fastaRecord.sequence = re.sub('[^%s]' % allowedLetters, 'N', fastaRecord.sequence)
fastaRecord.sequence = re.sub('[^%s-]' % allowedLetters, 'N',
fastaRecord.sequence)
# Print only if there is some sequence left:
if len(fastaRecord.sequence) > 0:
outputFile.write(str(fastaRecord) + "\n")
inputFile.close()
outputFile.close()
os.remove(tmpOutputFileName)
return inputFileList, sequenceCount, sequenceNameMap
def checkCacheConsistency(self, files):
idList = []
for inputFileName in files:
inputFile = open(inputFileName, 'r')
fastaIterator = Fasta.Iterator(inputFile,
parser=Fasta.RecordParser())
baseName = os.path.splitext(os.path.split(inputFileName)[-1])[0]
for fastaRecord in fastaIterator:
idList.append("%s_%s" % (baseName, fastaRecord.title))
pickleFileName = os.path.join(
self.options.project,
os.path.split(self.options.project)[1] + '.sap')
if os.path.exists(pickleFileName):
# See if the options have changed - and if they have:
# remove the selected parts of the cache.
pickleFile = open(pickleFileName, 'r')
prevOptions = pickle.load(pickleFile)
pickleFile.close()
# Lists of options that deprecates cache entries:
deleteBlastCacheList = [
"database", "maxblasthits", "limitquery", "minsignificance",
"nolowcomplexfilter", "blastwordsize"
]
#deleteHomologueCacheList = [ "unclassified", "notruncate", "quickcompile", "minidentity", "forceidentity", "subspecieslevel", "fillinall", "fillineven", "fillintomatch", "individuals", "significance", "nrsignificant",
deleteHomologueCacheList = [
"notruncate", "quickcompile", "minidentity", "forceidentity",
"subspecieslevel", "fillinall", "fillineven", "fillintomatch",
"individuals", "significance", "nrsignificant", "relbitscore",
"phyla", "classes", "orders", "families", "genera", "besthits",
"alignmentlimit", "minimaltaxonomy", "harddiversity",
"forceincludefile", "forceincludegilist", "forceexcludegilist"
]
deleteHomologueCacheList.extend(deleteBlastCacheList)
deleteAlignmentCacheList = ["alignment", "alignmentoption"]
deleteAlignmentCacheList.extend(deleteHomologueCacheList)
deleteTreesCacheList = []
deleteTreesCacheList.extend(deleteAlignmentCacheList)
deleteTreeStatsCacheList = ["assignment", "prunelevel"]
deleteTreeStatsCacheList.extend(deleteTreesCacheList)
print "Checking cache for deprecated entries"
for option in self.options.__dict__.keys():
# This serves to map between new and older option names:
prevVersionOption = option
if not prevOptions.__dict__.has_key(option):
if option == 'assignment':
prevVersionOption = 'sampler'
elif option == 'dbcache':
prevVersionOption = 'genbankcache'
elif option == 'minsignificance':
prevVersionOption = 'evaluecutoff'
elif option == 'significance':
prevVersionOption = 'evaluesignificance'
elif option == 'nrsignificant':
prevVersionOption = 'minsignificant'
else:
print "New option for SAP \"%s\" will take default value \"%s\"" % (
option, self.options.__dict__[option])
if option in deleteBlastCacheList and self.options.__dict__[
option] != prevOptions.__dict__[prevVersionOption]:
print '\tBlast cache'
for queryID in idList:
for entry in glob.glob(
os.path.join(self.options.blastcache, queryID)
+ '*'):
print "\t\t" + os.path.split(entry)[-1]
os.remove(entry)
deleteBlastCacheList = []
if option in deleteHomologueCacheList and self.options.__dict__[
option] != prevOptions.__dict__[prevVersionOption]:
# Delete the homologcache for the entries in the input files:
print '\tHomologue and alignment cache'
for queryID in idList:
for entry in glob.glob(
os.path.join(self.options.homologcache,
queryID) + '.*'):
print "\t\t" + os.path.split(entry)[-1]
os.remove(entry)
for entry in glob.glob(
os.path.join(self.options.alignmentcache,
queryID) + '.*'):
print "\t\t" + os.path.split(entry)[-1]
os.remove(entry)
deleteHomologueCacheList = []
if option in deleteTreesCacheList and self.options.__dict__[
option] != prevOptions.__dict__[prevVersionOption]:
# Delete the tree statistics cache for the entries in the input files:
print '\tTree sampling cache'
for queryID in idList:
for entry in glob.glob(
os.path.join(self.options.treescache, queryID)
+ '.*'):
print "\t\t" + os.path.split(entry)[-1]
os.remove(entry)
deleteTreesCacheList = []
if option in deleteTreeStatsCacheList and self.options.__dict__[
option] != prevOptions.__dict__[prevVersionOption]:
# Delete the tree statistics cache for the entries in the input files:
print '\tTree statistics cache'
for queryID in idList:
for entry in glob.glob(
os.path.join(self.options.treestatscache,
queryID) + '.*'):
print "\t\t" + os.path.split(entry)[-1]
os.remove(entry)
deleteTreeStatsCacheList = []
# Dump the options specified:
pickleFile = open(pickleFileName, 'w')
pickle.dump(self.options, pickleFile)
pickleFile.close()
print
def align(self, fastaFileName):
baseName = os.path.splitext(os.path.split(fastaFileName)[-1])[0]
alignmentFileName = os.path.join(self.options.alignmentcache,
baseName + ".nex")
print "%s: Alignment: " % baseName,
sys.stdout.flush()
if os.path.exists(
alignmentFileName) and os.path.getsize(alignmentFileName) > 0:
print "Using cached results."
sys.stdout.flush()
else:
print "Computing...",
sys.stdout.flush()
# Read in all the fasta entries:
fastaFile = open(fastaFileName, 'r')
fastaIterator = Fasta.Iterator(fastaFile,
parser=Fasta.RecordParser())
fastaDict = {}
for fastaRecord in fastaIterator:
fastaDict[fastaRecord.title] = fastaRecord.sequence
# Get the query sequence:
queryName = baseName
querySeq = fastaDict[queryName]
del fastaDict[queryName]
alignment = Nexus.Nexus()
seqList = [[queryName, Seq.Seq(querySeq)]]
for title, sequence in fastaDict.items():
alignmentList = pairwise2.align.globalms(querySeq,
sequence,
1,
0,
-10,
-.5,
one_alignment_only=1)
queryAlnString = alignmentList[0][0]
homologueAlnString = alignmentList[0][1]
# Delete the columns that introcudes gaps in the querySeq:
deleteList = []
for i, char in enumerate(queryAlnString):
if char == '-':
deleteList.append(i)
prunedHomologueAlnString = ''
for i, char in enumerate(homologueAlnString):
if i not in deleteList:
prunedHomologueAlnString += char
homologueAlnString = prunedHomologueAlnString
# Make a list of tuple with truncated title and Seq object and add it the list:
tup = (title, Seq.Seq(homologueAlnString))
seqList.append(tup)
# Write the alignment to a file:
writeNexusFile(alignmentFileName, seqList)
print "done",
sys.stdout.flush()
