From d59b1a3fcc02dd9f21dae684881a4c386d70bb97 Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Tue, 12 Aug 2014 15:24:56 +0200
Subject: [PATCH] cont. leipzig data processing
---
R/ggplot_utils.R | 3 ++-
bash/bioinfo_utils.sh | 49 +++++++++++++++++++++++++++++++++++++++
bash/lsf_bioinfo_utils.sh | 34 +++++++++++++++++++++++++++
3 files changed, 85 insertions(+), 1 deletion(-)
create mode 100644 bash/bioinfo_utils.sh
diff --git a/R/ggplot_utils.R b/R/ggplot_utils.R
index 1b12269..72fd7c1 100644
--- a/R/ggplot_utils.R
+++ b/R/ggplot_utils.R
@@ -37,4 +37,5 @@ makePcaPlot <- function(x = getData(), group = NA, items=rownames(x), title = ""
}
-makePcaPlot(getData(30,4,2,distort = 0.7), getGroup(30,2))
+## example
+# makePcaPlot(getData(30,4,2,distort = 0.7))
diff --git a/bash/bioinfo_utils.sh b/bash/bioinfo_utils.sh
new file mode 100644
index 0000000..bcf6307
--- /dev/null
+++ b/bash/bioinfo_utils.sh
@@ -0,0 +1,49 @@
+
+#### Tophat Mapping Report from the logs
+TophatMappingReport(){
+## todo replace source with simple R script as for bowtie-report
+echo '
+devtools::source_url("http://dl.dropbox.com/u/113630701/rlibs/deepseq/ngs_tools.R")
+createMappingReport()
+' | R -q --vanilla
+}
+
+#### Bowtie Mapping Report from the logs
+Bowtie2MappingReport(){
+
+echo '
+
+devtools::source_url("http://dl.dropbox.com/u/113630701/rlibs/base-commons.R")
+
+logSuffix=".logs"
+parseAlgnSummary <- function(alignSummary){
+ #alignSummary="./H2Az_Rep1_Lane1_Lib4454.bowtie.log"
+ algnData <- readLines(alignSummary)
+
+ data.frame(
+ condition=trimEnd(basename(alignSummary), logSuffix),
+ num_reads=as.numeric(str_split_fixed(algnData[3], " ", 2)[1]),
+ unique_mappers=as.numeric(str_split_fixed(str_trim(algnData[6]), " ", 2)[1]),
+ mapping_efficiency=as.numeric(str_replace(str_split_fixed(algnData[8], " ", 2)[1], "%", "")),
+ multi_mappers=as.numeric(str_split_fixed(str_trim(algnData[7]), " ", 2)[1])
+ )
+}
+
+mapStats <- ldply(list.files(".", logSuffix, full.names=TRUE, recursive=T), parseAlgnSummary, .progress="text")
+write.delim(mapStats, file="mapStats.txt")
+
+ggplot(melt(mapStats), aes(condition, value)) + geom_bar(stat="identity") +facet_wrap(~variable, scales="free") + ggtitle("mapping summary") + scale_y_continuous(labels=comma) + theme(axis.text.x=element_text(angle=90, hjust=0))
+ggsave2(w=10, h=10, p="mapstats")
+
+ggplot(mapStats, aes(condition, mapping_efficiency)) + geom_bar(stat="identity") +coord_flip() + ylim(0,100) + ggtitle("mapping efficiency")
+ggsave2(p="mapstats")
+ggplot(mapStats, aes(condition, num_reads)) + geom_bar(stat="identity") + coord_flip() + ggtitle("read counts")
+ggsave2(p="mapstats")
+
+ggplot(mapStats, aes(condition, unique_mappers)) + geom_bar(stat="identity") + coord_flip() + ggtitle("unique alignment") + scale_fill_discrete()
+ggsave2(p="mapstats")
+' | R --vanilla
+}
+export -f Bowtie2MappingReport
+
+
diff --git a/bash/lsf_bioinfo_utils.sh b/bash/lsf_bioinfo_utils.sh
index 31e518a..df3d2c7 100644
--- a/bash/lsf_bioinfo_utils.sh
+++ b/bash/lsf_bioinfo_utils.sh
@@ -1,4 +1,5 @@
+## create fastq report for all fastq and fastq.gz files in the current directory
mmFastqc(){
outputDir="fastqc_reports"
# filePattern="fastq.gz"
@@ -17,3 +18,36 @@ mmFastqc(){
}
export -f mmFastqc
+
+### Create a cuffdb on a network of lustre file-systen
+MakeCuffdb() {
+ if [ $# -ne 2 ]; then echo "Usage: MakeCuffdb <gtffile> <genomebuild>"; return; fi
+
+echo '
+devtools::source_url("http://dl.dropbox.com/u/113630701/rlibs/base-commons.R")
+options(width=150)
+
+require.auto(cummeRbund)
+
+createCuffDbTrickyDisk <- function(dbDir, gtfFile, genome, ...){
+ tmpdir <- tempfile()
+ system(paste("cp -r", dbDir, tmpdir))
+ oldWD <- getwd()
+ setwd(tmpdir)
+ cuff <- readCufflinks(rebuild=T, gtf=gtfFile, genome="mm10", ...)
+# cuff <- readCufflinks(gtf=gtfFile, genome="mm10", rebuild=T)
+
+ system(paste("cp cuffData.db", dbDir))
+ system(paste("rm -r", tmpdir))
+
+ setwd(oldWD)
+ return(cuff)
+}
+
+gtfFile=commandArgs(TRUE)[1]
+genomeBuild=commandArgs(TRUE)[2]
+
+createCuffDbTrickyDisk(getwd(), gtfFile, genomeBuild)
+' | R -q --no-save --no-restore --args $1 $2
+}
+export -f MakeCuffdb
--
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