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biopet.biopet
Commits
40ddc1b7
Commit
40ddc1b7
authored
Apr 25, 2017
by
pjvan_thof
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Fixing gearssingle report
parent
0740963c
Changes
2
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2 changed files
with
16 additions
and
6 deletions
+16
-6
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
...urces/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
+12
-2
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
+4
-4
No files found.
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
View file @
40ddc1b7
...
...
@@ -27,12 +27,22 @@
}
}#
<%
val summaries = summary.getStatsForSamples(runId, summaryModuleTag, summaryStatsTag, sampleId.map(SummaryDb.SampleId),
val summaries = if (libId.isDefined) summary.getStatsForLibraries(runId, summaryModuleTag, summaryStatsTag, sampleId,
Map("all" -> Nil)
).filter(_._1._2 == libId.get).map(x => x._1._1 -> x._2)
else summary.getStatsForSamples(runId, summaryModuleTag, summaryStatsTag, sampleId.map(SummaryDb.SampleId),
Map("all" -> Nil)
)
val totalReads = centrifugeTag.map { tag =>
summary.getStatsForSamples(runId, summaryModuleTag, ModuleName(tag), sampleId.map(SummaryDb.SampleId),
if (libId.isDefined) {
val stats = summary.getStatsForLibraries(runId, summaryModuleTag, ModuleName(tag), sampleId,
Map("total" -> List("metrics", "Read"))
).filter(_._1._2 == libId.get).head
val lib = allLibraries.filter(_.id == stats._1._2).head
val sample = allSamples.filter(_.id == stats._1._1).head
Map(s"${sample.name}" -> stats._2("total").map(_.toString.toLong).getOrElse(0L))
} else summary.getStatsForSamples(runId, summaryModuleTag, ModuleName(tag), sampleId.map(SummaryDb.SampleId),
Map("total" -> List("metrics", "Read"))
).map(x => allSamples.find(_.id == x._1).head.name -> x._2("total").map(_.toString.toLong).getOrElse(0L))
}
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
View file @
40ddc1b7
...
...
@@ -124,7 +124,7 @@ object GearsKraken {
val
taxs
:
mutable.Map
[
String
,
Any
]
=
mutable
.
Map
()
def
addTax
(
map
:
Map
[
String
,
Any
],
path
:
List
[
String
]
=
Nil
)
:
Unit
=
{
val
name
=
map
(
"n
ame"
).
toString
val
name
=
map
.
get
(
"name"
).
getOrElse
(
"noN
ame"
).
toString
val
x
=
path
.
foldLeft
(
taxs
)((
a
,
b
)
=>
if
(
a
.
contains
(
b
))
a
(
b
).
asInstanceOf
[
mutable.Map
[
String
,
Any
]]
else
{
a
+=
b
->
mutable
.
Map
[
String
,
Any
]()
a
(
b
).
asInstanceOf
[
mutable.Map
[
String
,
Any
]]
...
...
@@ -132,13 +132,13 @@ object GearsKraken {
if
(!
x
.
contains
(
name
))
x
+=
name
->
mutable
.
Map
[
String
,
Any
]()
map
(
"children"
).
asInstanceOf
[
List
[
Any
]].
foreach
(
x
=>
addTax
(
x
.
asInstanceOf
[
Map
[
String
,
Any
]],
path
:::
name
::
Nil
))
map
.
get
(
"children"
).
getOrElse
(
List
()
).
asInstanceOf
[
List
[
Any
]].
foreach
(
x
=>
addTax
(
x
.
asInstanceOf
[
Map
[
String
,
Any
]],
path
:::
name
::
Nil
))
}
summaries
.
foreach
{
x
=>
addTax
(
x
.
_2
(
"classified"
).
asInstanceOf
[
Map
[
String
,
Any
]])
}
summaries
.
foreach
{
x
=>
addTax
(
x
.
_2
.
get
(
"classified"
).
getOrElse
(
Map
()
).
asInstanceOf
[
Map
[
String
,
Any
]])
}
def
getValue
(
sample
:
String
,
path
:
List
[
String
],
key
:
String
)
=
{
path
.
foldLeft
(
summaries
(
sample
)
(
"classified"
).
asInstanceOf
[
Map
[
String
,
Any
]])
{
(
b
,
a
)
=>
path
.
foldLeft
(
summaries
(
sample
)
.
get
(
"classified"
).
getOrElse
(
Map
()
).
asInstanceOf
[
Map
[
String
,
Any
]])
{
(
b
,
a
)
=>
b
.
getOrElse
(
"children"
,
List
[
Map
[
String
,
Any
]]())
.
asInstanceOf
[
List
[
Map
[
String
,
Any
]]]
.
find
(
_
.
getOrElse
(
"name"
,
""
)
==
a
).
getOrElse
(
Map
[
String
,
Any
]())
...
...
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