def pairmodel(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("pairmodel --help")
return
persDir = inp.getPersistentDir()
outDir = inp.getOutputDir()
fo = inp.getFunctionOutput()
rsrc = Resources(inp.getInputValue("resources"))
rsrcFilename = os.path.join(persDir, 'rsrc.dat')
log.debug("Initializing pairmodel")
seq1 = inp.getInput('seq1')
seq2 = inp.getInput('seq2')
pdb1 = inp.getInput('pdb1')
pdb2 = inp.getInput('pdb2')
testseq = inp.getInput('testseq')
#how do we assign suffix name?
suffixname = pdb1.split('_')[-1]
if len(suffixname) > 3:
suffixname = suffixname[:-4]
#do we need to copy files to working directory?
if inp.getInput('cmdline_options') is not None:
if has_split:
cmdlineOpts = shutil.split(inp.getInput('cmdline_options'))
else:
cmdlineOpts = inp.getInput('cmdline_options').split()
else:
cmdlineOpts = []
# now add to the priority if this run has already been started
# we can always add state.cpt, even if it doesn't exist.
args = [
"--seqfile", testseq, "--template1", seq1, "--template2", seq2,
"--seqname",
os.path.basename(testseq)[:-4], "--samples1", pdb1, "--samples2", pdb2,
"--suffix", suffixname
]
args.extend(cmdlineOpts)
cmd = cpc.command.Command(newdirname, "modeltools/pairmodel", args)
if inp.hasInput("resources") and inp.getInput("resources") is not None:
log.debug("resources is %s" % (inp.getInput("resources")))
#rsrc=Resources(inp.getInputValue("resources"))
rsrc.updateCmd(cmd)
log.debug("Adding command")
fo.addCommand(cmd)
# and save for further invocations
rsrc.save(rsrcFilename)
return fo
def pairmodel(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("pairmodel --help")
return
persDir=inp.getPersistentDir()
outDir=inp.getOutputDir()
fo=inp.getFunctionOutput()
rsrc=Resources(inp.getInputValue("resources"))
rsrcFilename=os.path.join(persDir, 'rsrc.dat')
log.debug("Initializing pairmodel")
seq1=inp.getInput('seq1')
seq2=inp.getInput('seq2')
pdb1=inp.getInput('pdb1')
pdb2=inp.getInput('pdb2')
testseq=inp.getInput('testseq')
#how do we assign suffix name?
suffixname=pdb1.split('_')[-1]
if len(suffixname)>3:
suffixname=suffixname[:-4]
#do we need to copy files to working directory?
if inp.getInput('cmdline_options') is not None:
if has_split:
cmdlineOpts=shutil.split(inp.getInput('cmdline_options'))
else:
cmdlineOpts=inp.getInput('cmdline_options').split()
else:
cmdlineOpts=[]
# now add to the priority if this run has already been started
# we can always add state.cpt, even if it doesn't exist.
args=["--seqfile", testseq, "--template1", seq1, "--template2", seq2,
"--seqname", os.path.basename(testseq)[:-4], "--samples1", pdb1,
"--samples2", pdb2, "--suffix", suffixname ]
args.extend(cmdlineOpts)
cmd=cpc.command.Command(newdirname, "modeltools/pairmodel", args)
if inp.hasInput("resources") and inp.getInput("resources") is not None:
log.debug("resources is %s"%(inp.getInput("resources")))
#rsrc=Resources(inp.getInputValue("resources"))
rsrc.updateCmd(cmd)
log.debug("Adding command")
fo.addCommand(cmd)
# and save for further invocations
rsrc.save(rsrcFilename)
return fo
from cpc.dataflow import Value
from cpc.dataflow import FileValue
from cpc.dataflow import IntValue
from cpc.dataflow import FloatValue
from sets import Set
from cpc.dataflow import Resources
import cpc.command
import cpc.util
import tune
#hack to test for shutil.split()
has_split = True
try:
shutil.split('foo bar')
except:
has_split = False
class ModelError(cpc.util.CpcError):
pass
def pairmodel_multi(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("pairmodel --help")
return
pers = cpc.dataflow.Persistence(
from cpc.dataflow import Value
from cpc.dataflow import FileValue
from cpc.dataflow import IntValue
from cpc.dataflow import FloatValue
from sets import Set
from cpc.dataflow import Resources
import cpc.command
import cpc.util
import tune
#hack to test for shutil.split()
has_split=True
try:
shutil.split('foo bar')
except:
has_split=False
class ModelError(cpc.util.CpcError):
pass
def pairmodel_multi(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("pairmodel --help")
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
