def main():
sys.stderr.write("Arguments received : %s \n" % "_".join(sys.argv))
startTime = time.time()
alignerArgs = getDefaultArgs()
addDefaultArgs(alignerArgs)
addDefaultStitcherArgs(alignerArgs)
addDefaultNesterArgs(alignerArgs)
addDefaultEstimateTreeArgs(alignerArgs)
i = loggerIndices
removeReservedIndices(i, alignerArgs)
if len(sys.argv) < 3:
print "Ortheus.py [MODIFIER_ARGUMENTS]"
print "Version: ", VERSION_NO
print "A top level script for running Ortheus and Pecan to produce substitution and indel aware reconstructed chunks of genome"
print "If you would like to contribute to this program's development please contact me at bjp (AT) ebi (DOT) ac (DOT) uk "
print "Arguments:"
i = printFirstMods(alignerArgs, i)
i = printMods(alignerArgs, i)
i = printModsStitcher(alignerArgs, i)
i = printModsNester(alignerArgs, i)
i = printEstimateTreeMods(alignerArgs, i)
print "-------------Ortheus help string as follows (Changing these arguments may break the script)-------------"
os.system("ortheus_core")
print "-------------End Ortheus help string-------------"
print "-------------Pecan help string as follows (Changing these arguments may break the script)-------------"
os.system("%s bp.pecan.Pecan -help" % (alignerArgs.JAVA_PREFIX,))
print "-------------End Pecan help string-------------"
sys.exit(0)
mods = sys.argv[1:]
l = []
i = parseFirstMods(mods, alignerArgs, i, l)
i = parseMods(l, alignerArgs, i, mods)
i = parseModsStitcher(mods, alignerArgs, i, l)
i = parseModsNester(l, alignerArgs, i, mods)
i = parseEstimateTreeMods(mods, alignerArgs, i, l)
if len(l) != 0:
logger.info("Ooops, remaining arguments %s ", " ".join(l))
assert False
logger.info("Arguments received : %s " % " ".join(sys.argv))
logger.info("Sequence files : %s " % " ".join(alignerArgs.SEQUENCE_FILES))
if alignerArgs.EMPIRICALLY_ESTIMATE_CHARACTER_FREQUENCIES:
alignerArgs.EXPECTED_CHARACTER_FREQUENCIES = empiricallyEstimateNucleotideFrequencies(alignerArgs.SEQUENCE_FILES)
logger.info("Empirically estimated character frequencies : %s " % " ".join([ str(i) for i in alignerArgs.EXPECTED_CHARACTER_FREQUENCIES ]))
try:
os.remove(alignerArgs.OUTPUT_SCORE_FILE)
except OSError:
pass
if alignerArgs.NEWICK_TREE_STRING != None:
binaryTree = newickTreeParser(alignerArgs.NEWICK_TREE_STRING)
logger.info("Newick tree read : %s " % printBinaryTree(binaryTree, True))
else:
binaryTree, seqFiles, outputAlignment = estimateTreeAlign(alignerArgs.SEQUENCE_FILES, alignerArgs.OUTPUT_TREE_FILE, alignerArgs)
os.remove(outputAlignment) #for now, this should be
alignerArgs.SEQUENCE_FILES = seqFiles
if alignerArgs.MAKE_FINAL_ALIGNMENT:
nestAlign(binaryTree, alignerArgs.SEQUENCE_FILES, alignerArgs.OUTPUT_FILE, alignerArgs.OUTPUT_SCORE_FILE, alignerArgs)
#logger.info("Finished, total time taken : %s (seconds)" % (time.time()-startTime))
print "total_time %s " % (time.time()-startTime)
def makeAlignment(seqFiles, tree, outputAlignmentFile, alignerArgs):
if len(seqFiles) < 30:
makePecanAlignment(seqFiles, printBinaryTree(tree, True), outputAlignmentFile, alignerArgs)
else:
alignmentFile = getTempFile()
outputScoreFile = getTempFile()
nestAlign(tree, seqFiles, alignmentFile, outputScoreFile, alignerArgs)
splitOutAncestors(alignmentFile,outputAlignmentFile)
os.remove(alignmentFile)
os.remove(outputScoreFile)
def makeAlignment(seqFiles, tree, outputAlignmentFile, alignerArgs):
if len(seqFiles) < 30:
makePecanAlignment(seqFiles, printBinaryTree(tree, True),
outputAlignmentFile, alignerArgs)
else:
alignmentFile = getTempFile()
outputScoreFile = getTempFile()
nestAlign(tree, seqFiles, alignmentFile, outputScoreFile, alignerArgs)
splitOutAncestors(alignmentFile, outputAlignmentFile)
os.remove(alignmentFile)
os.remove(outputScoreFile)
