Commit 1d469ab5 by Eric Coissac

complete the graph compaction algorithm to provide more info

parent bd816dc2
......@@ -167,6 +167,4 @@ cdef class AsmbGraph(DiGraph):
return DiGraph.getNodeAttr(self, inode)
\ No newline at end of file
......@@ -144,7 +144,7 @@ def addOptions(parser):
'adapter sequences or internal set of adapter sequences '
'among %s' % (str(list(filter(lambda s: s.startswith('adapt3'),dir(orgasm.samples)))),) +' [default: %(default)s]' )
parser.add_argument('--seeds', dest ='orgasm:seeds',
parser.add_argument('--probes', dest ='orgasm:seeds',
metavar='seeds',
action='append',
default=[],
......
......@@ -9,7 +9,7 @@ from orgasm.tango import restoreGraph, estimateFragmentLength, genesincontig,\
from orgasm.version import version
__title__="Build a gfa file from the assembling graph"
__title__="Build a graph file from the assembling graph"
default_config = {
}
......@@ -22,25 +22,7 @@ def addOptions(parser):
nargs='?',
default=None,
help='output prefix' )
parser.add_argument('--path', dest='path:path',
action='store',
metavar='<edgeid>',
type=int,
nargs='+',
required=True,
default=None,
help='A list of edge id separated by space add -- at the end of the path')
parser.add_argument('--path-file', dest='path:pathfile',
action='store',
metavar='<filename>',
type=str,
default=None,
help='A filename containing a path to mark on the graph')
parser.add_argument('--back', dest='orgasm:back',
metavar='<insert size>',
type=int,
......
......@@ -12,7 +12,7 @@ from orgasm.tango import restoreGraph, estimateFragmentLength, genesincontig,\
__title__="Build a fasta file from a path across the assembling graph"
default_config = {
default_config = { "pathfile" : None
}
def addOptions(parser):
......
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