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biopet.biopet
Commits
066efc37
Commit
066efc37
authored
Jun 06, 2015
by
Peter van 't Hof
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Added library support
parent
cf653ddc
Changes
2
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2 changed files
with
33 additions
and
15 deletions
+33
-15
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+32
-14
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/XYPlot.scala
...scala/nl/lumc/sasc/biopet/extensions/rscript/XYPlot.scala
+1
-1
No files found.
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
066efc37
...
...
@@ -4,7 +4,7 @@ import java.io.{ PrintWriter, File }
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilder
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryValue
,
Summary
}
import
nl.lumc.sasc.biopet.extensions.rscript.
{
XYPlot
,
StackedBarPlot
}
import
nl.lumc.sasc.biopet.extensions.rscript.
{
XYPlot
,
StackedBarPlot
}
/**
* Created by pjvan_thof on 3/30/15.
...
...
@@ -89,19 +89,23 @@ object BammetricsReport extends ReportBuilder {
}
def
insertSizePlot
(
outputDir
:
File
,
prefix
:
String
,
summary
:
Summary
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
String
]
=
None
)
:
Unit
=
{
prefix
:
String
,
summary
:
Summary
,
libraryLevel
:
Boolean
=
false
,
sampleId
:
Option
[
String
]
=
None
)
:
Unit
=
{
val
tsvFile
=
new
File
(
outputDir
,
prefix
+
".tsv"
)
val
pngFile
=
new
File
(
outputDir
,
prefix
+
".png"
)
val
tsvWriter
=
new
PrintWriter
(
tsvFile
)
if
(
libraryLevel
)
{
tsvWriter
.
print
(
"Library"
)
tsvWriter
.
println
((
for
(
sample
<-
summary
.
samples
if
(
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
);
lib
<-
summary
.
libraries
(
sample
)
)
yield
s
"$sample-$lib"
)
.
mkString
(
"library\t"
,
"\t"
,
""
))
}
else
{
sampleId
match
{
case
Some
(
sample
)
=>
tsvWriter
.
println
(
"\t"
+
sample
)
case
_
=>
tsvWriter
.
println
(
summary
.
samples
.
mkString
(
"Sample\t"
,
"\t"
,
""
))
case
_
=>
tsvWriter
.
println
(
summary
.
samples
.
mkString
(
"Sample\t"
,
"\t"
,
""
))
}
}
...
...
@@ -109,14 +113,15 @@ object BammetricsReport extends ReportBuilder {
def
fill
(
sample
:
String
,
lib
:
Option
[
String
])
:
Unit
=
{
new
SummaryValue
(
List
(
"bammetrics"
,
"stats"
,
"CollectInsertSizeMetrics"
,
"histogram"
,
"content"
),
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
List
(
List
(
"insert_size"
,
"All_Reads.fr_count"
)))
match
{
case
l
:
List
[
_
]
=>
{
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
List
(
List
(
"insert_size"
,
"All_Reads.fr_count"
)))
match
{
case
l
:
List
[
_
]
=>
{
l
.
tail
.
foreach
(
_
match
{
case
l
:
List
[
_
]
=>
{
case
l
:
List
[
_
]
=>
{
val
insertSize
=
l
.
head
.
toString
.
toInt
val
count
=
l
.
tail
.
head
.
toString
.
toInt
val
old
=
map
.
getOrElse
(
insertSize
,
Map
())
map
+=
insertSize
->
(
old
+
((
sample
+
lib
.
getOrElse
(
""
))
->
count
))
if
(
libraryLevel
)
map
+=
insertSize
->
(
old
+
((
s
"$sample-"
+
lib
.
get
)
->
count
))
else
map
+=
insertSize
->
(
old
+
(
sample
->
count
))
}
case
_
=>
throw
new
IllegalStateException
(
"Must be a list"
)
})
...
...
@@ -125,12 +130,25 @@ object BammetricsReport extends ReportBuilder {
}
}
summary
.
samples
.
foreach
(
fill
(
_
,
None
))
if
(
libraryLevel
)
{
for
(
sample
<-
summary
.
samples
if
(
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
);
lib
<-
summary
.
libraries
(
sample
)
)
fill
(
sample
,
Some
(
lib
))
}
else
if
(
sampleId
.
isDefined
)
fill
(
sampleId
.
get
,
None
)
else
summary
.
samples
.
foreach
(
fill
(
_
,
None
))
for
((
insertSize
,
counts
)
<-
map
)
{
tsvWriter
.
print
(
insertSize
)
for
(
sample
<-
summary
.
samples
)
{
tsvWriter
.
print
(
"\t"
+
counts
.
getOrElse
(
sample
,
"0"
))
if
(
libraryLevel
)
{
for
(
sample
<-
summary
.
samples
if
(
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
);
lib
<-
summary
.
libraries
(
sample
)
)
tsvWriter
.
print
(
"\t"
+
counts
.
getOrElse
(
s
"$sample-$lib"
,
"0"
))
}
else
{
for
(
sample
<-
summary
.
samples
if
(
sampleId
.
isEmpty
||
sampleId
.
get
==
sample
))
{
tsvWriter
.
print
(
"\t"
+
counts
.
getOrElse
(
sample
,
"0"
))
}
}
tsvWriter
.
println
()
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/XYPlot.scala
View file @
066efc37
...
...
@@ -4,7 +4,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvan_thof on 4/29/15.
...
...
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