Commit be2c5ba6 by Eric Coissac

Add the logger to the call to scaffold

parent 6c213599
...@@ -415,7 +415,8 @@ def run(config): ...@@ -415,7 +415,8 @@ def run(config):
scaffold(asm,cg, scaffold(asm,cg,
minlink=5, minlink=5,
back=back, back=back,
addConnectedLink=False) addConnectedLink=False,
logger=logger)
with open(output+'.intermediate.gml','w') as gmlfile: with open(output+'.intermediate.gml','w') as gmlfile:
print(cg.gml(),file=gmlfile) print(cg.gml(),file=gmlfile)
...@@ -508,7 +509,13 @@ def run(config): ...@@ -508,7 +509,13 @@ def run(config):
cg = asm.compactAssembling(verbose=False) cg = asm.compactAssembling(verbose=False)
genesincontig(cg,r,x) genesincontig(cg,r,x)
scaffold(asm,cg,minlink=5,back=back,addConnectedLink=False) scaffold(asm,
cg,
minlink=5,
back=back,
addConnectedLink=False,
logger=logger)
with open(output+'.intermediate.gml','w') as gmlfile: with open(output+'.intermediate.gml','w') as gmlfile:
print(cg.gml(),file=gmlfile) print(cg.gml(),file=gmlfile)
...@@ -554,7 +561,8 @@ def run(config): ...@@ -554,7 +561,8 @@ def run(config):
cg = asm.compactAssembling(verbose=False) cg = asm.compactAssembling(verbose=False)
genesincontig(cg,r,x) genesincontig(cg,r,x)
scaffold(asm,cg,minlink=5,back=back,addConnectedLink=False) scaffold(asm,cg,minlink=5,back=back,addConnectedLink=False,
logger=logger)
with open(output+'.intermediate.gml','w') as gmlfile: with open(output+'.intermediate.gml','w') as gmlfile:
print(cg.gml(),file=gmlfile) print(cg.gml(),file=gmlfile)
...@@ -619,7 +627,8 @@ def run(config): ...@@ -619,7 +627,8 @@ def run(config):
cg = asm.compactAssembling(verbose=False) cg = asm.compactAssembling(verbose=False)
logger.info("Scaffold the assembly") logger.info("Scaffold the assembly")
scaffold(asm,cg,minlink=5,back=int(back),addConnectedLink=False) scaffold(asm,cg,minlink=5,back=int(back),addConnectedLink=False,
logger=logger)
genesincontig(cg,r,x) genesincontig(cg,r,x)
with open(output+'.gml','w') as gmlfile: with open(output+'.gml','w') as gmlfile:
print(cg.gml(),file=gmlfile) print(cg.gml(),file=gmlfile)
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