initial commit of dge workflow

R/core_commons.R

@@ -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

 ## 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

-## 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