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biopet.biopet
Commits
1b221835
Commit
1b221835
authored
Feb 03, 2015
by
bow
Browse files
Refactor and document fastqc data file parsing function
parent
c378965a
Changes
1
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public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
View file @
1b221835
...
...
@@ -25,27 +25,45 @@ import scalaz._, Scalaz._
import
nl.lumc.sasc.biopet.core.config.Configurable
class
Fastqc
(
root
:
Configurable
)
extends
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
Fastqc
(
root
)
{
def
getDataBlock
(
name
:
String
)
:
Array
[
String
]
=
{
// Based on Fastqc v0.10.1
/**
* FastQC QC modules.
*
* @return Mapping of FastQC module names and its contents as array of strings (one item per line)
* @throws FileNotFoundException if the FastQC data file can not be found.
* @throws IllegalStateException if the module mapping is empty.
*/
@throws
(
classOf
[
FileNotFoundException
])
@throws
(
classOf
[
IllegalStateException
])
protected
lazy
val
qcModules
:
Map
[
String
,
Array
[
String
]]
=
{
val
outputDir
=
output
.
getAbsolutePath
.
stripSuffix
(
".zip"
)
val
dataFile
=
new
File
(
outputDir
+
"/fastqc_data.txt"
)
if
(!
dataFile
.
exists
)
return
null
val
data
=
Source
.
fromFile
(
dataFile
).
mkString
for
(
block
<-
data
.
split
(
">>END_MODULE\n"
))
{
val
b
=
if
(
block
.
startsWith
(
"##FastQC"
))
block
.
substring
(
block
.
indexOf
(
"\n"
)
+
1
)
else
block
if
(
b
.
startsWith
(
">>"
+
name
))
return
for
(
line
<-
b
.
split
(
"\n"
))
yield
line
}
return
null
}
val
dataFile
=
new
File
(
outputDir
,
"fastqc_data.txt"
)
val
fqModules
=
Source
.
fromFile
(
dataFile
)
// drop all the characters before the first module delimiter (i.e. '>>')
.
dropWhile
(
_
!=
'>'
)
// pull everything into a string
.
mkString
// split into modules
.
split
(
">>END_MODULE\n"
)
// make map of module name -> module lines
.
map
{
case
(
modString
)
=>
// module name is in the first line, without '>>' and before the tab character
val
modName
=
modString
// so we take all characters in the first line
.
takeWhile
(
_
!=
'\n'
)
// and drop all characters that equals '>'
.
dropWhile
(
_
==
'>'
)
// and take all characters before the tab
.
takeWhile
(
_
!=
'\t'
)
modName
->
modString
.
split
(
'\n'
)
}
.
toMap
def
getEncoding
:
String
=
{
val
block
=
getDataBlock
(
"Basic Statistics"
)
if
(
block
==
null
)
return
null
for
(
line
<-
block
if
(
line
.
startsWith
(
"Encoding"
))
)
return
line
.
stripPrefix
(
"Encoding\t"
)
return
null
// Could be default Sanger with a warning in the log
if
(
fqModules
.
isEmpty
)
throw
new
IllegalStateException
(
"Empty FastQC data file "
+
dataFile
.
toString
)
else
fqModules
}
protected
case
class
Sequence
(
name
:
String
,
seq
:
String
)
...
...
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