Commit e2411f13 by Eric Coissac

dd a new clone command to copy and save an existing assembly with a new

parent a669250a
Created on 28 sept. 2014
@author: coissac
import orgasm.samples
from orgasm import getOutput,getIndex, getSeeds, getAdapters
from orgasm.tango import matchtoseed, cutLowCoverage, cutSNPs,\
estimateDeadBrancheLength, estimateFragmentLength,\
genesincontig, scaffold, fillGaps, dumpGraph, restoreGraph
from orgasm.assembler import Assembler,tango
import sys
import shutil
__title__="copy an assembly"
default_config = { "source" : None,
"dest" : None
def addOptions(parser):
parser.add_argument(dest='orgasm:outputfilename', metavar='outputfilename',
help='name of the assembly to be copied')
parser.add_argument(dest='clone:dest', metavar='dest',
help='name of the new copy of the assembly' )
def run(config):
progress = config['orgasm']['progress']
source = getOutput(config)"Copying the assembly %s to %s" % (config['orgasm']['outputfilename'],
shutil.copytree("%s.oas" % config['orgasm']['outputfilename'],
"%s.oas" % config['clone']['dest'])
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