Commit 5dd9fa97 by Eric Coissac

Comment the sam output option

parent c92d2785
...@@ -32,11 +32,11 @@ def addOptions(parser): ...@@ -32,11 +32,11 @@ def addOptions(parser):
default=None, default=None,
help='Wish a circular unfolding') help='Wish a circular unfolding')
parser.add_argument('--sam', dest='unfold:format', # parser.add_argument('--sam', dest='unfold:format',
action='store_const', # action='store_const',
const="sam", # const="sam",
default=None, # default=None,
help='Produce a SAM file of the assembly') # help='Produce a SAM file of the assembly')
parser.add_argument('--fasta', dest='unfold:format', parser.add_argument('--fasta', dest='unfold:format',
action='store_const', action='store_const',
...@@ -147,7 +147,8 @@ def run(config): ...@@ -147,7 +147,8 @@ def run(config):
path = path[-1][0] path = path[-1][0]
logger.info("Expanded path : %s" % str(path)) logger.info("Expanded path : %s" % str(path))
print("====>",config['unfold']['format'])
if config['unfold']['format']=="fasta": if config['unfold']['format']=="fasta":
fa = path2fasta(asm,cg,path, fa = path2fasta(asm,cg,path,
identifier="%s_%d" % (seqid,c), identifier="%s_%d" % (seqid,c),
......
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