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vidjil
vidjil
Commits
64e23fb6
Commit
64e23fb6
authored
Oct 11, 2018
by
Thonier Florian
Committed by
Mathieu Giraud
Oct 16, 2018
Browse files
pear_structured_log; move some line outside of the for loop
parent
b7238712
Changes
1
Hide whitespace changes
Inline
Side-by-side
tools/pear_structured_log.py
View file @
64e23fb6
...
...
@@ -5,6 +5,7 @@
# Script by Florian Thonier
# florian@vidjil.org
# ===============================
from
__future__
import
division
import
operator
import
sys
,
os
import
json
...
...
@@ -82,18 +83,20 @@ def pear_converter(fileIn, fileOut):
elif
"Not assembled reads"
in
line
:
json_data
[
"reads"
][
"reads_not_assembled_number"
]
=
int
(
convert_value
(
line
)[
0
].
replace
(
","
,
""
))
### Warnings
json_data
[
"warning"
]
=
[]
# assembled reads
percentage_not_assembled
=
json_data
[
"reads"
][
"reads_not_assembled_number"
]
/
json_data
[
"reads"
][
"reads_total_number"
]
if
percentage_not_assembled
>
50.00
:
json_data
[
"warning"
].
append
(
"Very few reads assembled"
)
elif
percentage_not_assembled
>
20.00
:
json_data
[
"warning"
].
append
(
"Few reads assembled"
)
# discarded reads
percentage_discarded
=
json_data
[
"reads"
][
"reads_discarded_number"
]
/
json_data
[
"reads"
][
"reads_total_number"
]
if
percentage_discarded
>
10.00
:
json_data
[
"warning"
].
append
(
"High level of discarded reads"
)
### Warnings
json_data
[
"warning"
]
=
[]
# assembled reads
percentage_not_assembled
=
int
(
json_data
[
"reads"
][
"reads_not_assembled_number"
])
/
json_data
[
"reads"
][
"reads_total_number"
]
json_data
[
"reads"
][
"percentage_not_assembled"
]
=
percentage_not_assembled
if
percentage_not_assembled
>
50.00
:
json_data
[
"warning"
].
append
(
"Very few reads assembled"
)
elif
percentage_not_assembled
>
20.00
:
json_data
[
"warning"
].
append
(
"Few reads assembled"
)
# discarded reads
percentage_discarded
=
json_data
[
"reads"
][
"reads_discarded_number"
]
/
json_data
[
"reads"
][
"reads_total_number"
]
json_data
[
"reads"
][
"percentage_discarded"
]
=
percentage_discarded
if
percentage_discarded
>
10.00
:
json_data
[
"warning"
].
append
(
"High level of discarded reads"
)
### export as json
...
...
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