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biopet.biopet
Commits
9b465609
Commit
9b465609
authored
Sep 09, 2015
by
Peter van 't Hof
Browse files
Change logging to logger.info
parent
a32bc102
Changes
2
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
View file @
9b465609
...
...
@@ -73,7 +73,7 @@ object SageCountFastq extends ToolCommand {
if
(
counts
.
contains
(
seq
))
counts
(
seq
)
+=
1
else
counts
+=
(
seq
->
1
)
count
+=
1
if
(
count
%
1000000
==
0
)
System
.
err
.
println
(
count
+
" sequences done"
)
if
(
count
%
1000000
==
0
)
logger
.
info
(
count
+
" sequences done"
)
}
})
logger
.
info
(
count
+
" sequences done"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
View file @
9b465609
...
...
@@ -117,21 +117,21 @@ object SageCreateLibrary extends ToolCommand {
tagRegex
=
(
commandArgs
.
tag
+
"[CATG]{"
+
commandArgs
.
length
+
"}"
).
r
var
count
=
0
System
.
err
.
println
(
"Reading fasta file"
)
logger
.
info
(
"Reading fasta file"
)
val
reader
=
FastaReaderHelper
.
readFastaDNASequence
(
commandArgs
.
input
)
System
.
err
.
println
(
"Finding tags"
)
logger
.
info
(
"Finding tags"
)
for
((
name
,
seq
)
<-
reader
)
{
val
result
=
getTags
(
name
,
seq
,
tagRegex
)
addTagresultToTaglib
(
name
,
result
)
count
+=
1
if
(
count
%
10000
==
0
)
System
.
err
.
println
(
count
+
" transcripts done"
)
if
(
count
%
10000
==
0
)
logger
.
info
(
count
+
" transcripts done"
)
}
System
.
err
.
println
(
count
+
" transcripts done"
)
logger
.
info
(
count
+
" transcripts done"
)
System
.
err
.
println
(
"Start sorting tags"
)
logger
.
info
(
"Start sorting tags"
)
val
tagGenesMapSorted
:
SortedMap
[
String
,
TagGenes
]
=
SortedMap
(
tagGenesMap
.
toArray
:
_
*
)
System
.
err
.
println
(
"Writting output files"
)
logger
.
info
(
"Writting output files"
)
val
writer
=
new
PrintWriter
(
commandArgs
.
output
)
writer
.
println
(
"#tag\tfirstTag\tAllTags\tFirstAntiTag\tAllAntiTags"
)
for
((
tag
,
genes
)
<-
tagGenesMapSorted
)
{
...
...
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