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biopet.biopet
Commits
9cb010e9
Commit
9cb010e9
authored
May 17, 2016
by
Peter van 't Hof
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Add gtf to refflat
parent
f297526c
Changes
3
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3 changed files
with
85 additions
and
2 deletions
+85
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
+41
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
.../scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
+39
-0
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
...sc/biopet/pipelines/generateindexes/GenerateIndexes.scala
+5
-2
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
0 → 100644
View file @
9cb010e9
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.util.matching.Regex
/**
* Created by pjvan_thof on 17-5-16.
*/
class
Awk
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
executable
=
config
(
"exe"
,
default
=
"awk"
,
freeVar
=
false
)
def
versionCommand
:
String
=
executable
+
" --version"
def
versionRegex
:
Regex
=
"""(GNU Awk \d+\.\d+\.\d+)"""
.
r
@Input
(
required
=
false
)
var
input
:
File
=
_
@Output
var
output
:
File
=
_
var
command
:
String
=
_
def
cmdLine
=
executable
+
required
(
command
)
+
(
if
(
inputAsStdin
)
""
else
required
(
input
))
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
}
object
Awk
{
def
apply
(
root
:
Configurable
,
command
:
String
)
:
Awk
=
{
val
awk
=
new
Awk
(
root
)
awk
.
command
=
command
awk
}
}
\ No newline at end of file
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
0 → 100644
View file @
9cb010e9
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvan_thof on 17-5-16.
*/
class
GtfToGenePred
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
executable
=
config
(
"exe"
,
default
=
"gtfToGenePred"
,
freeVar
=
false
)
@Input
var
inputGtfs
:
List
[
File
]
=
Nil
@Output
var
outputGenePred
:
File
=
_
@Output
var
infoOut
:
Option
[
File
]
=
None
var
genePredExt
:
Boolean
=
config
(
"gene _pred _ext"
,
default
=
false
)
var
allErrors
:
Boolean
=
config
(
"all_errors"
,
default
=
false
)
var
impliedStopAfterCds
:
Boolean
=
config
(
"implied_stop_after_cds"
,
default
=
false
)
var
simple
:
Boolean
=
config
(
"simple"
,
default
=
false
)
var
geneNameAsName2
:
Boolean
=
config
(
"gene _name_as_name2"
,
default
=
false
)
def
cmdLine
=
executable
+
conditional
(
genePredExt
,
"-genePredExt"
)
+
conditional
(
allErrors
,
"-allErrors"
)
+
optional
(
"-infoOut"
,
infoOut
)
+
conditional
(
allErrors
,
"-allErrors"
)
+
conditional
(
impliedStopAfterCds
,
"-impliedStopAfterCds"
)
+
conditional
(
simple
,
"-simple"
)
+
conditional
(
geneNameAsName2
,
"-geneNameAsName2"
)
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
outputGenePred
))
}
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
View file @
9cb010e9
...
...
@@ -208,9 +208,12 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
val
refFlatFile
:
Option
[
File
]
=
gtfFile
.
map
{
gtf
=>
val
refFlat
=
new
File
(
gtf
+
".refFlat"
)
//TODO: gtf to refFlat conversion
val
gtfToGenePred
=
new
GtfToGenePred
(
this
)
gtfToGenePred
.
inputGtfs
:+=
gtf
outputConfig
+=
"ribosome_refflat"
->
refFlat
add
(
gtfToGenePred
|
Awk
(
this
,
"""{ print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }"""
)
>
refFlat
)
outputConfig
+=
"annotation_refflat"
->
refFlat
refFlat
}
...
...
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