Commit 86341e86 by Eric Coissac

Adds the logger to the scaffold call

parent 219a4b08
......@@ -6,12 +6,14 @@ Created on 28 sept. 2014
import sys
from orgasm import getOutput,getIndex, getSeeds
from orgasm.tango import restoreGraph, estimateFragmentLength, genesincontig,\
pathConstraints, scaffold, selectGoodComponent, unfoldAssembling, path2fasta
pathConstraints, scaffold, selectGoodComponent, unfoldAssembling, path2fasta,\
path2sam
__title__="Universal assembling graph unfolder"
default_config = { 'circular' : False,
'force' : False
'force' : False,
'format' : "fasta"
}
def addOptions(parser):
......@@ -29,6 +31,18 @@ def addOptions(parser):
default=None,
help='Wish a circular unfolding')
parser.add_argument('--sam', dest='unfold:format',
action='store_const',
const="sam",
default=None,
help='Produce a SAM file of the assembly')
parser.add_argument('--fasta', dest='unfold:format',
action='store_const',
const="fasta",
default=None,
help='Produce a FASTA file of the assembly [default format]')
parser.add_argument('--force', dest='unfold:force',
action='store_true',
default=None,
......@@ -90,7 +104,8 @@ def run(config):
minlink=config['orgasm']['minlink']
constraints = pathConstraints(asm,cg,back=int(back),minlink=minlink)
scaffold(asm,cg,minlink=minlink,
back=int(back),addConnectedLink=False)
back=int(back),addConnectedLink=False,
logger=logger)
#fastaout = open(output+".fasta","w")
......@@ -101,7 +116,7 @@ def run(config):
logger.info("Select the good connected components")
gcc = selectGoodComponent(cg)
logger.info("Print the result as a fasta file")
logger.info("Print the result as a %s file" % config['unfold']['format'])
if config['unfold']['circular']:
if config['unfold']['force']:
......@@ -120,13 +135,22 @@ def run(config):
force=config['unfold']['force'])
path = path[-1][0]
fa = path2fasta(asm,cg,path,
identifier="%s_%d" % (seqid,c),
back=back,
minlink=config['orgasm']['minlink'],
logger=logger,
tags=config['fasta']['tags'])
if config['unfold']['format']=="fasta":
fa = path2fasta(asm,cg,path,
identifier="%s_%d" % (seqid,c),
back=back,
minlink=config['orgasm']['minlink'],
logger=logger,
tags=config['fasta']['tags'])
if config['unfold']['format']=="sam":
fa = path2sam(asm,cg,path,
identifier="%s_%d" % (seqid,c),
back=back,
minlink=config['orgasm']['minlink'],
logger=logger,
tags=config['fasta']['tags'])
print(fa,file=fastaout)
print(" ".join([str(x) for x in path]),file=pathout)
......
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