Commit e2411f13 by Eric Coissac

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

name
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):
logger=config['orgasm']['logger']
progress = config['orgasm']['progress']
source = getOutput(config)
logger.info("Copying the assembly %s to %s" % (config['orgasm']['outputfilename'],
config['clone']['dest']))
shutil.copytree("%s.oas" % config['orgasm']['outputfilename'],
"%s.oas" % config['clone']['dest'])
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