Merge pull request #4 from stjude/madetunj

more usage information

README.md

@@ -6,42 +6,49 @@ CLONED using SOURCETREE from: https://bitbucket.org/young_computation/rose/src/m
 
 
 #### === Changelog
-1) DIRECTORY structure
-
-    ├── LICENSE.txt
-
-    ├── README.md
-
-    ├── ROSE-call.sh    : bash wrapper
-
-    ├── lib
-
-        └── ROSE_utils.py   : utilities method
-    │   
-
-    └── src
-
-        ├── ROSE_bamToGFF.py    : calculates density of .bam reads in .gff regions
-
-        ├── ROSE_callSuper.R    : ranks regions by their densities, creates cutoff
-
-        ├── ROSE_geneMapper.py  : assigns stitched enhancers to genes
-
-        └── ROSE_main.py    : main program
-
-    Total: 2 directories, 8 files
-
-2) DEPENDENCIES
+1. USAGE
+
+	- Option 1: To run the program locally and independent of software location by calling ROSE-local.sh
+		NB: First open ROSE-local.sh and modify PATHTO with the PATH ROSE is installed in.
+		> ROSE-local.sh ["GTF file"] ["BAM file"] ["OutputDir"] ["feature type"] ["species"] ["bed fileA"] ["bed fileB"]
+
+	- Option 2: Add ROSE to user executable $PATH
+		```bash
+		PATHTO=/path/to/ROSE
+		PYTHONPATH=$PATHTO/lib
+		export PYTHONPATH
+		export PATH=$PATH:$PATHTO/bin
+		```
+
+1. Update: 
+
+	* ROSE is executable independent of software directory location.
+	* ROSE has a wrapper script "ROSE-local.sh" to successfully execute all steps of the package, else add ROSE to user executable $PATH
+	* ROSE is compatible with python3
+
+1. DIRECTORY structure
+	```
+	├── LICENSE.txt
+	│
+	├── README.md
+	│
+	├── ROSE-local.sh : bash wrapper
+	│
+	├── bin
+	│   ├── ROSE_bamToGFF.py : calculates density of .bam reads in .gff regions
+	│   ├── ROSE_callSuper.R : ranks regions by their densities, creates cutoff
+	│   ├── ROSE_geneMapper.py : assigns stitched enhancers to genes
+	│   └── ROSE_main.py : main program
+	└── lib
+	    └── ROSE_utils.py : utilities method
+
+	Total: 2 directories, 8 files
+	```
+1. DEPENDENCIES
 
 	* samtools
 	* R version > 3.4
 	* bedtools > 2
 	* python3
 
-3) USAGE
-
-Program is run by calling ROSE-call.sh
-NB: First modify PATHTO with your own directory. 
-> ROSE-call.sh ["GTF file"] ["BAM file"] ["OutputDir"] ["feature type"] ["species"] ["bed fileA"] ["bed fileB"]
-
 =================================================================

ROSE-local.sh

@@ -0,0 +1,99 @@
+#!/bin/bash
+#
+# Rose Caller to detect both Enhancers and Super-Enhancers
+#
+# Version 1 11/16/2019
+
+##############################################################
+# ##### Please replace PATHTO with your own directory ###### #
+##############################################################
+PATHTO=/path/to/ROSE
+PYTHONPATH=$PATHTO/lib
+export PYTHONPATH
+export PATH=$PATH:$PATHTO/bin
+
+if [ $# -lt 7 ]; then
+  echo ""
+  echo 1>&2 Usage: $0 ["GTF file"] ["BAM file"] ["OutputDir"] ["feature type"] ["species"] ["bed fileA"] ["bed fileB"]
+  echo ""
+  exit 1
+fi
+
+#================================================================================
+#Parameters for running
+
+# GTF files
+GTFFILE=$1
+
+# BAM file
+BAMFILE=$2
+
+# Output Directory
+OUTPUTDIR=$3
+OUTPUTDIR=${OUTPUTDIR:=ROSE_out}
+
+# Feature type
+FEATURE=$4
+FEATURE=${FEATURE:=gene}
+
+# Species
+SPECIES=$5
+SPECIES=${SPECIES:=hg_19}
+
+# Bed File A
+FILEA=$6
+
+# Bed File B
+FILEB=$7
+
+# Transcription Start Size Window
+#TSS=
+TSS=${TSS:=2000}
+
+# Maximum linking distance for stitching
+#STITCH=
+STITCH=${STITCH:=12500}
+
+
+echo "#############################################"
+echo "######             ROSE v1             ######"
+echo "#############################################"
+
+echo "Input Bed File A: $FILEA"
+echo "Input Bed File B: $FILEB"
+echo "BAM file: $BAMFILE"
+echo "Output directory: $OUTPUTDIR"
+echo "Species: $SPECIES"
+echo "Feature type: $FEATURE"
+#================================================================================
+# 
+# GENERATING UCSC REFSEQ FILE
+#
+mkdir -p annotation
+echo -e "#bin\tname\tchrom\tstrand\ttxStart\ttxEnd\tcdsStart\tcdsEnd\tX\tX\tX\t\tX\tname2" > annotation/$SPECIES"_refseq.ucsc"
+
+if [[ $FEATURE == "gene" ]]; then
+awk -F'[\t ]' '{
+  if($3=="gene")
+    print "0\t" $14 "\tchr" $1 "\t" $7 "\t" $4 "\t" $5 "\t" $4 "\t" $5 "\t.\t.\t.\t.\t" $18}' $GTFFILE | sed s/\"//g >> annotation/$SPECIES"_refseq.ucsc"
+
+elif [[ $FEATURE == "transcript" ]]; then
+awk -F'[\t ]' '{
+  if($3=="transcript")
+    print "0\t" $14 "\tchr" $1 "\t" $7 "\t" $4 "\t" $5 "\t" $4 "\t" $5 "\t.\t.\t.\t.\t" $18}' $GTFFILE | sed s/\"//g >> annotation/$SPECIES"_refseq.ucsc"
+fi
+echo "Annotation file: "$SPECIES"_refseq.ucsc"
+
+#
+# GENERATING MERGE BED FILES
+#
+cat $FILEA $FILEB | sort -k1,1 -k2,2n | mergeBed -i - | awk -F\\t '{print $1 "\t" NR "\t\t" $2 "\t" $3 "\t\t.\t\t" NR}' > unionpeaks.gff
+echo "Merge Bed file: unionpeaks.gff"
+echo
+
+#
+# ROSE CALLER
+#
+ROSE_main.py -s $STITCH -t $TSS -g $SPECIES -i unionpeaks.gff -r $BAMFILE -o $OUTPUTDIR
+
+echo "Done!"