modernized chipseq utilities

chipseq_workflow/chipseq_utils.sh

@@ -136,7 +136,7 @@ if [ $# -ne 2 ]; then
 fi
 
 echo '
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R")
 
 bamFile=commandArgs(T)[1]
 chromInfoFile=commandArgs(T)[2]
@@ -144,9 +144,12 @@ chromInfoFile=commandArgs(T)[2]
 #bamFile="/projects/bioinfo/holger/projects/krause_chipseq/alignments_mmfilt/H3HA_Dome_mmf.bam";
 #chromInfoFile="danRer7.chromInfo"
 
+#bamFile="/projects/bioinfo/holger/projects/krause_chipseq/reanalysis/../alignments_mmfilt/H3HA_Sphere_mmf.bam";
+#chromInfoFile="danRer7.chromInfo"
+
 chrOrderBam <- readLines(pipe(paste("samtools view -H ", bamFile, " | cut -f2 | grep -F SN"))) %>% str_replace(fixed("SN:"), "")
 
-chromInfo <- read.delim(chromInfoFile) %>% mutate(chrom=str_replace(chrom, "chr", ""))
+chromInfo <- read_tsv(chromInfoFile, col_names=F) %>% set_names("chromosome", "chr_length") %>% mutate(chrom=str_replace(chromosome, "chr", ""))
 
 #data.frame(chrom=chrOrderBam) %>%
 #    left_join(chromInfo) %>%
@@ -154,16 +157,15 @@ chromInfo <- read.delim(chromInfoFile) %>% mutate(chrom=str_replace(chrom, "chr"
 #    mutate(size=ifelse(is.na(size), -1, size)) %>%
 #    write.delim(stdout(), header=F, quote=F)
 
-read.delim(chromInfoFile) %>%
-    mutate(chrom=str_replace(chrom, "chrM", "MT")) %>%
-    mutate(chrom=str_replace(chrom, "chr", "")) %>%
-    mutate(chrom=factor(as.character(chrom), levels=chrOrderBam)) %>% arrange(chrom) %>%
-    filter(!is.na(chrom)) %>%
+read_tsv(chromInfoFile, col_names=F) %>%
+    set_names("chromosome", "chr_length") %>%
+    mutate(chromosome=str_replace(chromosome, "chrM", "MT") %>% str_replace("chr", "")) %>%
+    mutate(chromosome=factor(as.character(chromosome), levels=chrOrderBam)) %>% arrange(chromosome) %>%
+    filter(!is.na(chromosome)) %>%
     write.delim(stdout(), header=F, quote=F)
 ' | Rscript --vanilla - $1 $2  2> /dev/null
 }
-export -f cs_sync_order_chrominfo2bam
-
+cs_sync_order_bam2bed
 
 cs_sync_order_bam2bed(){
 
@@ -172,7 +174,7 @@ if [ $# -ne 2 ]; then
 fi
 
 echo '
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R")
 
 bamFile=commandArgs(T)[1]
 bedFile=commandArgs(T)[2]

dge_workflow/dge_utils.sh

@@ -14,6 +14,7 @@ export PATH=${BIO_BIN_BASE}/FastQC_0.11.2:$PATH
 export PATH=${BIO_BIN_BASE}/bedtools2-2.25.0/bin/:$PATH
 export PATH=${BIO_BIN_BASE}/samtools-1.3:$PATH
 export PATH=${BIO_BIN_BASE}/STAR-2.5.1b/source:$PATH
+export PATH=${BIO_BIN_BASE}/ucsc:$PATH # for wigToBigWig
 #export PATH=/home/brandl/bin/subread-1.4.6-p3-Linux-x86_64/bin:$PATH
 
 

pom.xml

@@ -6,6 +6,10 @@
     <groupId>de.mpicbg.scicomp.bioinfo</groupId>
     <version>1.0-SNAPSHOT</version>
 
+    <properties>
+        <kotlin.version>1.0.3</kotlin.version>
+    </properties>
+
 
     <dependencies>
         <dependency>
@@ -25,5 +29,45 @@
             <artifactId>kutils</artifactId>
             <version>0.1-SNAPSHOT</version>
         </dependency>
+        <dependency>
+            <groupId>org.jetbrains.kotlin</groupId>
+            <artifactId>kotlin-stdlib</artifactId>
+            <version>${kotlin.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.jetbrains.kotlin</groupId>
+            <artifactId>kotlin-test</artifactId>
+            <version>${kotlin.version}</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
+
+    <build>
+        <sourceDirectory></sourceDirectory>
+        <plugins>
+            <plugin>
+                <groupId>org.jetbrains.kotlin</groupId>
+                <artifactId>kotlin-maven-plugin</artifactId>
+                <version>${kotlin.version}</version>
+                <executions>
+                    <execution>
+                        <id>compile</id>
+                        <phase>process-sources</phase>
+                        <goals>
+                            <goal>compile</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>test-compile</id>
+                        <phase>process-test-sources</phase>
+                        <goals>
+                            <goal>test-compile</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+
 </project>
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