Commit 154194fd by Eric Coissac

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parent b7098a6b
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'''
Created on 28 sept. 2014
@author: coissac
'''
from orgasm import getIndex, getSeeds
from orgasm.tango import restoreGraph, estimateFragmentLength, genesincontig,\
pathConstraints, scaffold, selectGoodComponent, unfoldAssembling, path2fasta
__title__="Index a set of reads"
default_config = { 'single' : False,
'maxread' : None,
'length' : None,
'estimate' : None,
'fasta' : False
}
def addOptions(parser):
parser.add_argument(dest='orgasm:indexfilename', metavar='index',
help='name of the produced index')
parser.add_argument(dest='index:forward', metavar='forward',
help='Filename of the forward reads')
parser.add_argument(dest='index:reverse', metavar='reverse',
nargs='?',
default=None,
help='Filename of the reverse reads' )
parser.add_argument('--single', dest='index:single',
action='store_true',
default=None,
help='Force circular unfolding')
parser.add_argument('--max-read', dest='index:maxread',
type=int,
action='store',
default=None,
help='the count of million of reads to '
'index (default the full file)')
parser.add_argument('--length', dest='index:length',
type=int,
action='store',
default=None,
help='The length of the read to index '
' (default indexed length is estimated from the first read)')
parser.add_argument('--estimate-length', dest='index:estimate',
meta='FRACTION',
type=float,
action='store',
default=None,
help='Estimate the length to index for conserving FRACTION '
'of the overall dataset')
parser.add_argument('--fasta', dest='index:fasta',
action='store_true',
default=None,
help='Force circular unfolding')
def run(config):
logger=config['orgasm']['logger']
output = config['orgasm']['outputfilename']
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