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vidjil
vidjil
Commits
35923d65
Commit
35923d65
authored
Oct 05, 2018
by
Vidjil
Browse files
sample_set.py: read ratio decorator
parent
fde77ed6
Changes
1
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Inline
Side-by-side
server/web2py/applications/vidjil/controllers/sample_set.py
View file @
35923d65
...
...
@@ -665,8 +665,8 @@ def getStatHeaders():
l
=
LociListDecorator
()
return
[(
'sample_sets'
,
'db'
,
s
),
(
'main_clone'
,
'parser'
,
m
),
(
'reads'
,
'parser'
,
m
),
(
'mapped'
,
'parser'
,
m
),
#
('reads', 'parser', m),
(
'mapped
reads
'
,
'parser'
,
m
),
(
'mapped_percent'
,
'parser'
,
p
),
(
'read lengths'
,
'parser'
,
g
),
#('bool', 'parser', b),
...
...
@@ -695,8 +695,9 @@ def getFusedStats(file_name, res, dest):
result_index
=
data
[
'samples'
][
'original_names'
].
index
(
defs
.
DIR_SEQUENCES
+
res
[
'sequence_file'
])
dest
[
'main_clone'
]
=
data
[
'clones'
][
0
][
'name'
]
reads
=
data
[
'reads'
][
'total'
][
result_index
]
dest
[
'reads'
]
=
reads
dest
[
'mapped'
]
=
"%d"
%
(
data
[
'reads'
][
'segmented'
][
result_index
])
# dest['reads'] = reads
mapped_reads
=
data
[
'reads'
][
'segmented'
][
result_index
]
dest
[
'mapped reads'
]
=
"%d / %d (%.2f %%)"
%
(
mapped_reads
,
reads
,
100.0
*
mapped_reads
/
reads
if
reads
else
0
)
dest
[
'mapped_percent'
]
=
100.0
*
(
float
(
data
[
'reads'
][
'segmented'
][
result_index
])
/
float
(
reads
))
dest
[
'abundance'
]
=
[(
key
,
100.0
*
data
[
'reads'
][
'germline'
][
key
][
result_index
]
/
reads
)
for
key
in
data
[
'reads'
][
'germline'
]]
...
...
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