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genotoul-bioinfo
D-GENIES
Commits
fbf557c3
Commit
fbf557c3
authored
Feb 02, 2018
by
Floreal Cabanettes
Browse files
Remove debug
parent
6d9fc4db
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/dgenies/lib/paf.py
View file @
fbf557c3
...
...
@@ -484,21 +484,15 @@ class Paf:
return
percents
def
_remove_overlaps
(
self
,
position_idy
:
IntervalTree
,
percents
:
dict
):
i
=
0
#position_idy_final = []
while
len
(
position_idy
)
>
0
:
item
=
position_idy
.
pop
()
# print("ITEM", item)
start
=
item
.
begin
end
=
item
.
end
if
len
(
position_idy
)
==
1331
:
k
=
"stop"
# bidon
cat
=
item
.
data
overlaps
=
position_idy
.
search
(
start
,
end
)
if
len
(
overlaps
)
>
0
:
has_overlap
=
False
for
overlap
in
overlaps
:
#print("OVERLAP", overlap)
if
has_overlap
:
break
o_start
=
overlap
.
begin
...
...
@@ -506,8 +500,6 @@ class Paf:
o_cat
=
overlap
.
data
if
not
position_idy
.
containsi
(
o_start
,
o_end
,
o_cat
):
continue
if
o_start
==
101099524
and
o_end
==
101104878
:
k
=
"stop"
# bidon
if
start
<
o_start
:
if
end
<=
o_end
:
# cccccccccccccc*******
...
...
@@ -618,7 +610,6 @@ class Paf:
Get summary of identity
:return: table with percents by category
"""
print
(
"P1"
)
summary_file
=
self
.
paf
+
".summary"
self
.
parse_paf
(
False
,
False
)
if
self
.
parsed
:
...
...
@@ -636,15 +627,8 @@ class Paf:
percents
=
self
.
_remove_overlaps
(
position_idy
,
percents
)
print
(
"P2"
)
print
(
percents
)
for
cat
in
percents
:
percents
[
cat
]
=
percents
[
cat
]
/
self
.
len_t
*
100
print
(
self
.
len_t
)
print
(
"P4"
)
with
open
(
summary_file
,
"w"
)
as
summary_file
:
summary_file
.
write
(
json
.
dumps
(
percents
))
...
...
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