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biopet.biopet
Commits
e3400a8a
Commit
e3400a8a
authored
Jan 25, 2017
by
Peter van 't Hof
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Added unassigned reads to krona plot for centrifuge
parent
67a6842b
Changes
6
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6 changed files
with
18 additions
and
12 deletions
+18
-12
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+1
-1
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
...urces/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
+8
-2
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
+2
-2
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+3
-3
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
.../lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
+1
-1
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+3
-3
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
e3400a8a
...
...
@@ -120,7 +120,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
val
className
=
if
(
f
.
getClass
.
isAnonymousClass
)
f
.
getClass
.
getSuperclass
.
getSimpleName
else
f
.
getClass
.
getSimpleName
BiopetQScript
.
safeOutputs
(
f
)
match
{
case
Some
(
o
)
=>
f
.
jobOutputFile
=
new
File
(
o
.
head
.
getAbsoluteFile
.
getParent
,
"."
+
f
.
firstOutput
.
getName
+
"."
+
className
+
".out"
)
case
_
=>
f
.
jobOutputFile
=
new
File
(
"./stdout"
)
// Line is here for test backup
case
_
=>
f
.
jobOutputFile
=
new
File
(
"./stdout"
)
// Line is here for test backup
}
})
...
...
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
View file @
e3400a8a
...
...
@@ -10,17 +10,23 @@
<%@ var libId: Option[String] = None %>
<%@ var args: Map[String, Any] %>
<%@ var outputDir: File %>
<%@ var centrifugeTag: Option[String] = None %>
<%@ var summaryStatsTag: String = "krakenreport" %>
<%@ var summaryModuleTag: String = "gearskraken" %>
<%
val summaries = if (sampleId.isEmpty
&& libId.isEmpty
) {
val summaries = if (sampleId.isEmpty) {
summary.getSampleValues(summaryModuleTag, "stats", summaryStatsTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
} else summary.getValue(sampleId, libId, summaryModuleTag, "stats", summaryStatsTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
val totalReads = if (sampleId.isEmpty) {
centrifugeTag.map {tag => summary.getSampleValues(summaryModuleTag, "stats", tag, "metrics", "Read").map(x => x._1 -> x._2.getOrElse(0L).toString.toLong) }
} else centrifugeTag.flatMap(tag => summary.getValue(sampleId, libId, summaryModuleTag, "stats", tag, "metrics", "Read"))
.map(value => Map(sampleId.get -> value.toString.toLong))
val tempFile = File.createTempFile("krona.", ".xml")
tempFile.deleteOnExit()
GearsKraken.convertKrakenSummariesToKronaXml(summaries, tempFile)
GearsKraken.convertKrakenSummariesToKronaXml(summaries, tempFile
, totalReads
)
val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/krona.ssp",
args ++ Map("kronaXml" -> tempFile))
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
View file @
e3400a8a
...
...
@@ -120,7 +120,7 @@ object GearsKraken {
convertKrakenSummariesToKronaXml
(
summaries
,
outputFile
)
}
def
convertKrakenSummariesToKronaXml
(
summaries
:
Map
[
String
,
Map
[
String
,
Any
]],
outputFile
:
File
)
:
Unit
=
{
def
convertKrakenSummariesToKronaXml
(
summaries
:
Map
[
String
,
Map
[
String
,
Any
]],
outputFile
:
File
,
totalReads
:
Option
[
Map
[
String
,
Long
]]
=
None
)
:
Unit
=
{
val
samples
=
summaries
.
keys
.
toList
.
sorted
...
...
@@ -156,7 +156,7 @@ object GearsKraken {
if
(
k
==
"root"
)
{
val
unclassified
=
summaries
(
sample
)(
"unclassified"
).
asInstanceOf
[
Map
[
String
,
Any
]](
"size"
).
asInstanceOf
[
Long
]
<
val
>
{
getValue
(
sample
,
(
path
:::
k
::
Nil
).
tail
,
"size"
).
getOrElse
(
0
).
toString
.
toLong
+
unclassified
}
{
totalReads
.
flatMap
(
_
.
get
(
sample
)).
getOrElse
(
getValue
(
sample
,
(
path
:::
k
::
Nil
).
tail
,
"size"
).
getOrElse
(
0
).
toString
.
toLong
+
unclassified
)
}
</
val
>
}
else
{
<
val
>
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
e3400a8a
...
...
@@ -50,7 +50,7 @@ object GearsReport extends MultisampleReportBuilder {
)),
Map
())),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
)))
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
...
...
@@ -92,7 +92,7 @@ object GearsReport extends MultisampleReportBuilder {
)),
Map
())),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
)))
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
...
...
@@ -126,7 +126,7 @@ object GearsReport extends MultisampleReportBuilder {
)),
Map
())),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
)))
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
View file @
e3400a8a
...
...
@@ -41,7 +41,7 @@ object GearsSingleReport extends ReportBuilder {
else
Nil
)
++
(
if
(
centrifugeExecuted
)
List
(
"Centrifuge analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"summaryStatsTag"
->
"centrifuge_unique_report"
)))
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"summaryStatsTag"
->
"centrifuge_unique_report"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)
)))
else
Nil
),
pageArgs
)
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
e3400a8a
...
...
@@ -65,7 +65,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
)),
Map
())),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
)))
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)
)))
else
Nil
)
++
List
(
"Reference"
->
ReportPage
(
List
(),
List
(
"Reference"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/reference.ssp"
,
Map
(
"pipeline"
->
pipelineName
))
...
...
@@ -128,7 +128,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Libraries"
->
generateLibraryPage
(
args
),
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
None
))
++
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
ReportPage
(
List
(
"Non-unique"
->
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
Map
(
"summaryStatsTag"
->
"centrifuge_report"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)
)
)),
Map
())),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
...
...
@@ -162,7 +162,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
)),
Map
())),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
)))
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
...
...
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