def main(args):
parser = OptionParser('usage: %prog [options]')
optionsAvailable = (
('-i', '--input', 'Sequence_File_ID', 'int',
'Sequence_File_ID from MegaChip.Sequence_File table.'),
('-a', '--alignment', 'Alignment_Protocol_ID', 'int',
('Alignment_Protocol_ID from MegaChip.Alignment_Protocol '
'table.')),
('-t', '--taxonomy', 'Taxonomy_ID', 'int',
'Taxonomy_ID from MegaChipDB.Taxonomy table.'),
('-e','--expect','Alignment_Score_Limit','float',
'Score cutoff for alignment.'),
('-f', '--filter', 'Blast_Filter_Protocol_ID', 'int',
('Blast_Filter_Protocol_ID from MegaChipDB.'
'Blast_Filter_Protocol table. If None no filter will be '
'used.')),
('-l', '--likeTHD', 'templateTHD_ID','int',
'use exsiting THD as template for unspecified values'),
)
ids =[ x[2] for x in optionsAvailable if x[2] != 'templateTHD_ID' ]
for opt in optionsAvailable:
if opt[3] is None:
otype = 'string'
else:
otype = opt[3]
parser.add_option(opt[0], opt[1], dest=opt[2], type=otype,
help=opt[4])
(options, args) = parser.parse_args(args)
defined = lambda x: getattr(options, x) is not None
if options.templateTHD_ID != None:
templateTHD=THD(options.templateTHD_ID)
for opt in ids:
if not defined(opt):
setattr(options,opt,getattr(templateTHD,opt))
if not all(map(defined, ids)):
print >> sys.stderr, ('Usage error: all arguments are required, '
'or derived from template THD')
print >> sys.stderr, parser.format_help()
sys.exit(1)
thdc = THDCreator(options.Sequence_File_ID,
options.Alignment_Protocol_ID,
options.Alignment_Score_Limit,
options.Taxonomy_ID,
options.Blast_Filter_Protocol_ID)
thdc.run()
def main(args):
parser = OptionParser('usage: %prog [options]')
optionsAvailable = (
('-i', '--input', 'Sequence_File_ID', 'int',
'Sequence_File_ID from MegaChip.Sequence_File table.'),
('-a', '--alignment', 'Alignment_Protocol_ID', 'int',
('Alignment_Protocol_ID from MegaChip.Alignment_Protocol '
'table.')),
('-t', '--taxonomy', 'Taxonomy_ID', 'int',
'Taxonomy_ID from MegaChipDB.Taxonomy table.'),
('-e','--expect','Alignment_Score_Limit','float',
'Score cutoff for alignment.'),
('-f', '--filter', 'Blast_Filter_Protocol_ID', 'int',
('Blast_Filter_Protocol_ID from MegaChipDB.'
'Blast_Filter_Protocol table. If None no filter will be '
'used.')),
('-l', '--likeTHD', 'templateTHD_ID','int',
'use exsiting THD as template for unspecified values'),
)
ids =[ x[2] for x in optionsAvailable if x[2] != 'templateTHD_ID' ]
for opt in optionsAvailable:
if opt[3] is None:
otype = 'string'
else:
otype = opt[3]
parser.add_option(opt[0], opt[1], dest=opt[2], type=otype,
help=opt[4])
(options, args) = parser.parse_args(args)
defined = lambda x: getattr(options, x) is not None
if options.templateTHD_ID != None:
templateTHD=THD(options.templateTHD_ID)
for opt in ids:
if not defined(opt):
setattr(options,opt,getattr(templateTHD,opt))
if not all(map(defined, ids)):
print >> sys.stderr, ('Usage error: all arguments are required, '
'or derived from template THD')
print >> sys.stderr, parser.format_help()
sys.exit(1)
thdc = THDCreator(options.Sequence_File_ID,
options.Alignment_Protocol_ID,
options.Alignment_Score_Limit,
options.Taxonomy_ID,
options.Blast_Filter_Protocol_ID)
outputFiles = thdc.allOutputFilenames()
print outputFiles
script = ('python %s/removeDups.py -i%%(INinitial)s '
'-o%%(OUTnoDups)s -s%%(seqFileId)s' % SCRIPTS_FOLDER)
remDupsDesc = JobDescription(Command=script, insertIfNeeded=True)
remDupsJob = Job(Job_Description_ID=remDupsDesc,
INinitial=str(thdc.sequenceFile()),
OUTnoDups=outputFiles[0],
seqFileId=thdc._sequenceFileID)
script = ('python %s/filterQuality.py -i%%(INnoDups)s '
'-o%%(OUTqualFiltered)s -s%%(seqFileId)s' %
SCRIPTS_FOLDER)
filQualDesc = JobDescription(Command=script, insertIfNeeded=True)
filQualJob = Job(Job_Description_ID=filQualDesc,
INnoDups=remDupsJob.outputs[0],
OUTqualFiltered=outputFiles[1],
seqFileId=thdc._sequenceFileID)
outputVars = {}
tmpOutVars = []
for idx, outFn in enumerate(outputFiles[2]):
n = 'OUTfile%d' % idx
outputVars[n] = outFn
tmpOutVars.append('%%(%s)s' % n)
script = ('python %s/applyBlastFilters.py -i%%(INqualFiltered)s '
'-s%%(seqFileId)s -f%%(filterId)s %s' %
(SCRIPTS_FOLDER, ' '.join(tmpOutVars)))
blastFilterDesc = JobDescription(Command=script,
insertIfNeeded=True)
blastFilterJob = Job(Job_Description_ID=blastFilterDesc,
INqualFiltered=filQualJob.outputs[0],
seqFileId=thdc._sequenceFileID,
filterId=thdc._filterProtocolID,
**outputVars)
script = ('python %s/doAlignment.py -i%%(INfilteredFile)s '
'-o%%(OUTmbrFile)s -a%%(alignProtocolId)s' %
SCRIPTS_FOLDER)
mbrDesc = JobDescription(Command=script, insertIfNeeded=True)
script = ('python %s/createThd.py -i%%(INmbrFile)s '
'-s%%(seqFileId)s -x%%(filterindex)s '
'-a%%(alignProtocolId)s -t%%(taxonomyId)s '
'-e%%(scoreLimit)s -f%%(filterId)s' % SCRIPTS_FOLDER)
thdDesc = JobDescription(Command=script, insertIfNeeded=True)
addJobs = []
for idx, filteredFile in enumerate(outputFiles[2]):
mbrJob = Job(Job_Description_ID=mbrDesc,
INfilteredFile=filteredFile,
OUTmbrFile=outputFiles[3][idx],
alignProtocolId=thdc._alignmentProtocolID)
thdJob = Job(Job_Description_ID=thdDesc,
INmbrFile=mbrJob.outputs[0],
seqFileId=thdc._sequenceFileID, filterindex=idx,
alignProtocolId=thdc._alignmentProtocolID,
taxonomyId=thdc._taxonomyDBID,
scoreLimit=thdc._scoreCutoff,
filterId=thdc._filterProtocolID)
addJobs.append(mbrJob)
addJobs.append(thdJob)
jm = JobManager([remDupsJob, filQualJob, blastFilterJob] + \
addJobs)
jm.buildTree()
jm.run()
print 'Root JobManager: %d' % int(jm)
