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ORG.Asm
ORG.Asm
Commits
678d54be
Commit
678d54be
authored
Apr 11, 2016
by
Eric Coissac
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Use logger instead of direct print to stderr
parent
3d4c982e
Changes
1
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1 changed file
with
23 additions
and
20 deletions
+23
-20
python/orgasm/assembler/_assembler.pyx
python/orgasm/assembler/_assembler.pyx
+23
-20
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python/orgasm/assembler/_assembler.pyx
View file @
678d54be
...
...
@@ -6,10 +6,10 @@ from orgasm.indexer._orgasm cimport *
from
._asmbgraph
cimport
*
from
._assembler
cimport
*
from
orgasm.graph._graphmultiedge
cimport
*
from
functools
import
reduce
from
orgasm.apps.progress
cimport
ProgressBar
from
orgasm.apps.config
cimport
getConfiguration
from
orgasm.utils.dna
cimport
reverseComplement
import
math
...
...
@@ -219,10 +219,8 @@ cpdef dict buildstem(Assembler assembler,
}
if
circle
:
print
(
" Circle : %6d bp coverage : %6dx"
%
(
length
,
int
(
w
)),
file
=
sys
.
stderr
)
getConfiguration
()[
'orgasm'
][
'logger'
].
info
(
" Circle : %6d bp coverage : %6dx"
%
(
length
,
int
(
w
)))
return
s
...
...
@@ -249,7 +247,10 @@ cdef class CompactAssembling(DiGraphMultiEdge):
cdef
double
minweight
cdef
AsmbGraph
graph
cdef
dict
stem
cdef
dict
config
=
getConfiguration
()
logger
=
config
[
'orgasm'
][
'logger'
]
DiGraphMultiEdge
.
__init__
(
self
,
'compact'
)
self
.
_paths
=
{}
...
...
@@ -262,7 +263,7 @@ cdef class CompactAssembling(DiGraphMultiEdge):
if
verbose
:
print
(
"Compacting graph :"
,
file
=
sys
.
stderr
)
logger
.
info
(
"Compacting graph :"
)
else
:
progress
=
ProgressBar
(
lgraph
,
head
=
"Compacting graph"
,
...
...
@@ -282,17 +283,15 @@ cdef class CompactAssembling(DiGraphMultiEdge):
minweight
=
weight
if
verbose
:
print
(
" Stem : %6d bp (total : %6d) coverage : %6.2f"
%
(
stem
[
'length'
],
lcontig
,
weight
),
file
=
sys
.
stderr
)
logger
.
info
(
" Stem : %6d bp (total : %6d) coverage : %6.2f"
%
(
stem
[
'length'
],
lcontig
,
weight
))
else
:
progress
(
lcontig
)
self
.
setStemid
()
print
(
"
\n
Minimum stem coverage = %d"
%
int
(
minweight
),
file
=
sys
.
stderr
)
logger
.
info
(
"Minimum stem coverage = %d"
%
int
(
minweight
))
...
...
@@ -593,20 +592,23 @@ cdef class Assembler:
cdef
int32_t
i
# @DuplicatedSignature
cdef
set
ep
cdef
set
sp
graph
=
self
.
graph
cd
=
0
d
=
1
print
(
''
,
file
=
sys
.
stderr
)
if
sys
.
stderr
.
isatty
():
print
(
''
,
file
=
sys
.
stderr
)
while
d
>
0
:
d
=
0
for
i
in
self
.
endNodeSet
(
alllink
=
alllink
):
print
(
"Remaining edges : %d node : %d"
%
(
graph
.
edgeCount
(),
len
(
graph
)),
end
=
'
\r
'
,
file
=
sys
.
stderr
)
if
sys
.
stderr
.
isatty
():
print
(
"Remaining edges : %d node : %d"
%
(
graph
.
edgeCount
(),
len
(
graph
)),
end
=
'
\r
'
,
file
=
sys
.
stderr
)
d
+=
deleteBranch
(
graph
,[
i
],
maxlength
)
cd
+=
d
...
...
@@ -620,9 +622,10 @@ cdef class Assembler:
except
KeyError
:
pass
print
(
"Remaining edges : %d node : %d"
%
(
graph
.
edgeCount
(),
len
(
graph
)),
end
=
'
\r
'
,
file
=
sys
.
stderr
)
if
sys
.
stderr
.
isatty
():
print
(
"Remaining edges : %d node : %d"
%
(
graph
.
edgeCount
(),
len
(
graph
)),
end
=
'
\r
'
,
file
=
sys
.
stderr
)
return
cd
...
...
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