Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
D
datautils
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Locked Files
Issues
1
Issues
1
List
Boards
Labels
Service Desk
Milestones
Merge Requests
0
Merge Requests
0
Requirements
Requirements
List
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Security & Compliance
Security & Compliance
Dependency List
License Compliance
Operations
Operations
Environments
Packages & Registries
Packages & Registries
Package Registry
Container Registry
Analytics
Analytics
CI / CD
Code Review
Insights
Issue
Repository
Value Stream
Wiki
Wiki
Snippets
Snippets
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Create a new issue
Jobs
Commits
Issue Boards
Open sidebar
bioinfo
datautils
Commits
8a595336
Commit
8a595336
authored
Nov 14, 2014
by
Holger Brandl
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
initial commit of dge workflow
parent
eb740601
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
with
2 additions
and
179 deletions
+2
-179
R/core_commons.R
R/core_commons.R
+1
-0
R/utils/spinr.R
R/utils/spinr.R
+1
-12
bash/lsf_rna_seq.sh
bash/lsf_rna_seq.sh
+0
-167
No files found.
R/core_commons.R
View file @
8a595336
...
...
@@ -190,6 +190,7 @@ rmerge <- function(LDF, by, ...){
trim_ext
<-
function
(
fileNames
,
...
)
trimEnd
(
fileNames
,
...
)
trimEnd
<-
function
(
fileNames
,
exts
=
c
()){
for
(
fileExt
in
exts
){
fileNames
<-
str_replace
(
fileNames
,
paste
(
fileExt
,
"$"
,
sep
=
""
),
""
)
...
...
R/utils/spinr.R
View file @
8a595336
## a thin wrapper around spin to make it more useful with more custom output
require
(
knitr
)
require
(
stringr
)
...
...
@@ -7,14 +8,6 @@ options(width=150)
#https://groups.google.com/forum/#!topic/knitr/ojcnq5Nm298
## better table css: http://www.stat.ubc.ca/~jenny/STAT545A/topic10_tablesCSS.html
#setwd("/local/home/brandl/mnt/mack/project-raphael/reports/spin_report")
#setwd("/home/brandl/mnt/mack/project-raphael/reports/spin_report")
#rScript='/home/brandl/mnt/mack/project-raphael/Rcode/misc/DivisionPerpendicularity.R'
#rScript='/home/brandl/mnt/mack/project-raphael/Rcode/misc/Test.R'
#spinr <- function(rScript){
spin
(
rScript
,
knit
=
F
)
mdScript
<-
str_replace
(
rScript
,
"[.]R$"
,
".Rmd"
)
...
...
@@ -36,7 +29,3 @@ opts_chunk$set(cache = TRUE, fig.width=10, width=120)
knit2html
(
basename
(
mdScript
),
header
=
cssHeader
)
file.remove
(
basename
(
mdScript
))
#}
# spinr("/home/brandl/mnt/mack/project-raphael/Rcode/misc/DivisionPerpendicularity.R")
# spinr("/home/brandl/mnt/mack/project-raphael/Rcode/misc/Test.R")
bash/lsf_rna_seq.sh
deleted
100644 → 0
View file @
eb740601
## docs
## http://blog.joncairns.com/2013/08/what-you-need-to-know-about-bash-functions/
## create fastq report for all fastq and fastq.gz files in the current directory
dge_fastqc
(){
while
getopts
"o:"
curopt
;
do
case
$curopt
in
o
)
outputDir
=
$OPTARG
;
esac
done
shift
$((
$OPTIND
-
1
))
local
fastqFiles
=
$*
#if [ -z "$fastqFiles" ]; then
if
[
$#
-lt
1
]
;
then
echo
"Usage: dge_fastqc [-o <output_directory>] [<fastq.gz file>]+"
>
&2
;
return
;
fi
## use default directory if not specified
if
[
-z
"
$outputDir
"
]
;
then
outputDir
=
"fastqc_reports"
fi
if
[
!
-d
"
$outputDir
"
]
;
then
echo
"creating output directory '
$outputDir
'"
mkdir
$outputDir
fi
for
fastqFile
in
$fastqFiles
;
do
echo
"fastqcing
$fastqFile
"
if
[
!
-f
$fastqFile
]
;
then
continue
;
fi
mysub
"fastqc__
$(
basename
$fastqFile
)
"
"fastqc -j /sw/bin/java -o
$outputDir
-f fastq
$fastqFile
"
-q
medium | joblist .fastqc_jobs
done
wait4jobs .fastqc_jobs
mailme
"fastqc done for
$outputDir
"
# todo create some summary report here
}
export
-f
dge_fastqc
#http://wiki.bash-hackers.org/howto/getopts_tutorial
dge_tophat_se
(){
# http://stackoverflow.com/questions/18414054/bash-getopts-reading-optarg-for-optional-flags
echo
$*
while
getopts
"i:"
curopt
;
do
case
$curopt
in
i
)
IGENOME
=
"
$OPTARG
"
;
esac
done
shift
$((
$OPTIND
-
1
))
local
fastqFiles
=
$*
echo
fastq
$fastqFiles
echo
igenomes
"
$IGENOME
"
if
[
-z
"
$IGENOME
"
]
||
[
-z
"
$fastqFiles
"
]
;
then
echo
"Usage: dge_tophat_se -i <path to igenome> [<fastq.gz file>]+"
>
&2
;
return
;
fi
export
bowtie_gindex
=
"
$IGENOME
/Sequence/Bowtie2Index/genome"
export
gtfFile
=
"
$IGENOME
/Annotation/Genes/genes.gtf"
#head $gtfFile
if
[
!
-f
$gtfFile
]
;
then
>
&2
echo
"gtf '
$gtfFile
' does not exis"
;
return
;
fi
if
[
-z
"
$(
which tophat
)
"
]
;
then
>
&2
echo
"no tomcat binary in PATH"
;
return
;
fi
echo
"running tophat using igenome '
$IGENOME
' for the following files"
ll
$fastqFiles
#fastqFiles=$(ls $baseDir/treps_pooled/*fastq.gz)
for
fastqFile
in
$fastqFiles
;
do
echo
"submitting tophat job for
$fastqFile
"
# DEBUG fastqFile=/projects/bioinfo/holger/projects/eric/trimmed/a1_ca.fastq.gz
fastqBaseName
=
$(
basename
${
fastqFile
%%.fastq.gz
}
)
outputdir
=
$fastqBaseName
## uniquely mapping reads only: http:/seqanswers.com/forums/showthread.php?s=93da11109ae12a773a128a637d69defe&t=3464
mysub
"
${
project
}
__tophat__
${
fastqBaseName
}
"
"
tophat -p6 -G
$gtfFile
-g1 -o
$outputdir
$bowtie_gindex
$fastqFile
mv
$outputdir
/accepted_hits.bam
$outputdir
/
$(
basename
$outputdir
)
.bam
samtools index
$outputdir
/
$(
basename
$outputdir
)
.bam
"
-n
5
-R
span[hosts
=
1]
-q
long | joblist .tophatjobs
done
wait4jobs .tophatjobs
## create tophat mapping report
source
<
(
curl https://dl.dropboxusercontent.com/u/113630701/datautils/bash/bioinfo_utils.sh 2>&1 2>/dev/null
)
TophatMappingReport
}
export
-f
dge_tophat_se
# dge_tophat_se
# dge_tophat_se -i
dge_cuffdiff
(){
local
gtfFile
=
$1
local
bamDir
=
$2
local
labels
=
$3
if
[
$#
-ne
3
]
;
then
echo
"Usage: dge_fastqc <gtf_file> <bam directory> <labels>"
>
&2
;
return
;
fi
if
[
-z
"
$(
which cuffdiff
)
"
]
;
then
>
&2
echo
"no cuffdiff binary in PATH"
;
return
;
fi
if
[
!
-f
$gtfFile
]
;
then
>
&2
echo
"gtf '
$gtfFile
' does not exis"
;
return
;
fi
## collect all bam-files and group them
allBams
=
$(
find
$bamDir
|
grep
".bam$"
|
grep
-v
"unmapped"
|
sort
)
bamsSplit
=
""
for
label
in
$(
echo
$labels
|
tr
", "
" "
)
;
do
echo
$label
labelBams
=
$(
echo
"
$allBams
"
|
grep
$label
| xargs
echo
-n
|
tr
' '
','
)
bamsSplit+
=
$labelBams
" "
done
#echo $bamsSplit
## make sure (again that all files are there
echo
$gtfFile
$bamsSplit
|
tr
","
" "
| xargs
ls
-la
#mysub ${project}_cuffdiff "cuffdiff -L aRGm,aRGp,aRG,bRG,IPC,N -o . -p 8 mm10_ensGene_ccds.gtf $amBams $apBams $aBams $bBams $cBams $dBams 2>&1 | tee cuffdiff.log" -q long -n 8 -R span[hosts=1] | blockScript
cdCmd
=
"cuffdiff -L
$labels
-o . -p 10
$gtfFile
$bamsSplit
"
#echo "cmd is: $cdCmd"
mysub
${
project
}
__cuffdiff
"
$cdCmd
"
-q
long
-n
8
-R
span[hosts
=
1] | blockScript
MakeCuffDB
$gtfFile
"NAN"
}
\ No newline at end of file
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment