sync

naumenko-sa · May 17, 2019 · b384be7 · b384be7
1 parent e66d284
commit b384be7
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Showing 6 changed files with 7 additions and 8 deletions.
diff --git a/scripts/__pycache__/AddJunctionsToDatabase.cpython-35.pyc b/scripts/__pycache__/AddJunctionsToDatabase.cpython-35.pyc
diff --git a/scripts/crt.bam2junctions.pbs b/scripts/crt.bam2junctions.pbs
@@ -9,8 +9,8 @@ CRT_HOME='/home/naumenko/crt'
 
 if [ -z "$genes" ]
 then
-	genes=$CRT_HOME/genes.bed
+	genes=$CRT_HOME/data/genes.bed
 fi
 
 module load python/3.5.2
-python3 $CRT_HOME/SpliceJunctionDiscovery.py -genes=$genes -bam=$bam
+python3 $CRT_HOME/scripts/SpliceJunctionDiscovery.py -genes=$genes -bam=$bam
diff --git a/scripts/crt.filter_junctions.sh b/scripts/crt.filter_junctions.sh
@@ -13,6 +13,6 @@ then
     bam=$1
 fi
 
-python3 ~/crt/FilterSpliceJunctions.py --sample $bam 5 0.05
+python3 ~/crt/scripts/FilterSpliceJunctions.py --sample $bam 5 0.05
 
 cat ${bam}_specific_rc5_norm_rc0.05_n_gtex_184 | grep -v BOTH > $bam.rare_junctions.txt
diff --git a/scripts/crt.load_junctions.pbs b/scripts/crt.load_junctions.pbs
@@ -10,7 +10,7 @@ CRT_HOME='/home/naumenko/crt'
 module load python/3.5.2
 module load sqlite/3.20.0
 
-python3 $CRT_HOME/AddJunctionsToDatabase.py \
+python3 $CRT_HOME/scripts/AddJunctionsToDatabase.py \
 	--addBAM \
 	-bam=$bam \
 	-flank=2
diff --git a/scripts/crt.mds.pbs b/scripts/crt.mds.pbs
@@ -5,4 +5,4 @@
 #PBS -d .
 #PBS -l vmem=20g,mem=20g
 
-Rscript ~/crt/crt.naumenko2018.R $refresh
+Rscript ~/crt/scripts/crt.mds.R mds_work $refresh
diff --git a/scripts/crt.utils.R b/scripts/crt.utils.R
@@ -243,13 +243,13 @@ feature_counts2rpkm <- function(filename){
     # filename <- "S100_47-1-Myo.bam.feature_counts.txt"
     # first line in the file is a comment
     counts <- read_tsv(filename, skip = 1) %>% 
-                select(Geneid, Length, last_col()) %>% 
+                dplyr::select(Geneid, Length, last_col()) %>% 
                 rename(ensembl_gene_id = Geneid, length = Length)
     colnames(counts) <- gsub(".bam","", colnames(counts))
 
     sample_name <- colnames(counts)[3]
     counts$rpkm <- rpkm(counts[,sample_name], counts$length)
-    counts <- counts %>% select(ensembl_gene_id, rpkm) %>% rename(!!sample_name := rpkm)
+    counts <- counts %>% dplyr::select(ensembl_gene_id, rpkm) %>% rename(!!sample_name := rpkm)
     return(counts)
 }
 
@@ -747,7 +747,6 @@ if (length(args) == 0 || args[1] == "--help"){
     cat("splicing.read_novel_splice_events sample.bam.rare_junctions.txt\n")
 }else{
     cat(paste0("Running function: ", args[1],"\n"))
-    init()
     fcn <- get(args[1])
     fcn(tail(args,-1))
 }