Merge pull request #6 from mahmoudibrahim/mahmoudibrahim-patch-1

Mahmoudibrahim patch 1

JAMM.sh

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud M Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################
 
 
@@ -28,7 +28,7 @@ sPath="`( cd \"$sPath\" && pwd )`"
 usage()
 {
 cat << EOF
-Welcome to JAMM v1.0.7rev5 (GNU GPLv3). Copyright (C) 2014-2016  Mahmoud Ibrahim.
+Welcome to JAMM v1.0.7rev5 (GNU GPLv3). Copyright (C) 2014-2019  Mahmoud Ibrahim.
 
 This program comes with ABSOLUTELY NO WARRANTY; for details visit http://www.gnu.org/licenses/gpl.html. This is free software, and you are welcome to redistribute it under certain conditions; visit http://www.gnu.org/licenses/gpl.html for details.
 
@@ -136,23 +136,44 @@ then
      usage
      exit 1
 fi
-if [[ -d "$out/peaks" ]]; then
-	printf "\n\nOutput directory $out/peaks already exists. I can't override existing results!\n\n"
+if [ -f "$out/peaks/filtered.peaks.narrowPeak"  ]; then
+	printf "\n\nOutput file $out/peaks/filtered.peaks.narrowPeak already exists. I can't override existing results!\n\n"
 	exit 0
 fi
+
 if [ $fraglen == "ns" ]; then
-	if [[ -d "$out/xcorr" ]]; then
-		printf "\n\nOutput directory $out/xcorr already exists. I can't override existing results!\n\n"
-		exit 0
-	fi
+	for j in $out/xcorr/*/xcorrsummary.txt; do
+		if [ -e "$j" ]; then
+			printf "\n\nOutput files in $out/xcorr already exist. I can't override existing results!\n\n"
+			exit 0
+		fi
+	done
 fi
+
 nreps=$(ls -1 $sdir/*.bed | wc -l) #count how many sample files
 #no sample files
 if [ $nreps == "0" ]; then
 	echo "No Sample Files Found!"
 	exit 1
 fi
 
+if [ $fraglen != "ns" ]; then
+	IFS=',' read -ra numTemp <<< "$fraglen"
+	numFrags=$(echo "${#numTemp[@]}")
+	if [ $bdir != "None" ]; then
+		nrepsTemp=$(echo $((nreps + 1)))
+		if [ $numFrags != $nrepsTemp ]; then
+			printf "\n\nThe number of fragment lengths you gave is not the same as the number of sample replicates (and background). There should be as many fragment lengths as number of sample replicates+1\n\n"
+			exit 1
+		fi
+	else
+		if [ $numFrags != $nreps ]; then
+			printf "\n\nThe number of fragment lengths you gave is not the same as the number of sample replicates. There should be as many fragment lengths as there are sample replicates\n\n"
+			exit 1
+		fi
+	fi
+fi
+
 if [ $tempdir == "/tmp" ]; then
 	wdir=$(mktemp -d -t -p $tempdir)
 else
@@ -245,8 +266,9 @@ if [ $fraglen == "ns" ]; then
 
 	##Counting Where Reads Start and Calculating Cross Correlation
 	mkdir $wdir/stats.$ran/ #store count files
-	mkdir $out/xcorr #final xcorr results
-
+	if [ ! -d "$out/xcorr" ]; then
+		mkdir $out/xcorr #final xcorr results
+	fi
 
 	printf "Calculating Fragment Length(s)...\n"
 	for f in $wdir/sizes.$ran/*; do #for each chromosome
@@ -290,15 +312,19 @@ if [ $fraglen == "ns" ]; then
 	for f in $sdir/*.bed; do
 		file=$(basename $f)
 		samplefile=$(echo $file | awk -F"." '{print $1}');	
-		mkdir "$out/xcorr/$samplefile" #final xcorr results
+		if [ ! -d "$out/xcorr/$samplefile" ]; then
+			mkdir "$out/xcorr/$samplefile" #final xcorr results
+		fi
 		if [ -f "$wdir/stats.$ran/xc.$samplefile.tab" ]; then
 			cp $wdir/stats.$ran/xc.$samplefile.tab $out/xcorr/$samplefile/shifts.txt	
 		fi
 		Rscript "$sPath/xcorrhelper.r" -infile="$out/xcorr/$samplefile/shifts.txt" -out="$out/xcorr/$samplefile"
 	done
 	#report xcorr results (control)
 	if [ $bdir != "None" ]; then
-		mkdir "$out/xcorr/ctrl" #final xcorr results
+		if [ ! -d "$out/xcorr/ctrl" ]; then
+			mkdir "$out/xcorr/ctrl" #final xcorr results
+		fi
 		if [ -f "$wdir/stats.$ran/xc.ctrl.tab" ]; then
 			cp $wdir/stats.$ran/xc.ctrl.tab $out/xcorr/ctrl/shifts.txt
 		fi
@@ -382,8 +408,9 @@ fi
 # Step Four: Calling Peaks
 # ===========================
 mkdir $wdir/peaks.$ran/ #store count files
-mkdir $out/peaks #store peak files
-
+if [ ! -d "$out/peaks" ]; then
+	mkdir $out/peaks #store peak files
+fi
 printf "Calling Peaks...(mode: $mode, resolution: $resol)\n"
 
 

README.md

@@ -1,18 +1,18 @@
 JAMM Peak Finder
 ======
 
-**JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets. Read more [in JAMM's publication](http://bioinformatics.oxfordjournals.org/content/early/2014/09/15/bioinformatics.btu568).** 
+**JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets. Read more [in JAMM's publication](https://academic.oup.com/bioinformatics/article/31/1/48/2365061).** 
 
-JAMM was developed at the [Ohler lab](http://ohlerlab.mdc-berlin.net/) at [BIMSB-MDC](http://www.mdc-berlin.de/13800178/en/bimsb) in Berlin.
+JAMM was developed at the [Ohler lab](http://ohlerlab.mdc-berlin.net/) at [BIMSB-MDC](https://www.mdc-berlin.de/bimsb) in Berlin.
 
-If you have questions or need help running JAMM please email us at [this email](http://www.google.com/recaptcha/mailhide/d?k=01vPijd2GG0LEbZV2NyE_rSA==&c=49GEiFp47dZQV_120clczwxYcP3tQ98VWBJtNl6_dBw=), we will be happy to help you.
+If you have questions or need help running JAMM please email us at [this email](http://scr.im/jammpro), we will be happy to help you.
 
 
 
 Download JAMM
 ------
 
-**The latest JAMM version is _JAMMv1.0.7rev5_. [Click here to download it](https://github.com/mahmoudibrahim/JAMM/archive/JAMMv1.0.7.5.zip).**
+**The latest JAMM version is _JAMMv1.0.7rev6_. [Click here to download it](https://github.com/mahmoudibrahim/JAMM/archive/JAMMv1.0.7.6.zip).**
 
 If you are interested in older versions, check the [Downloads Archive](https://github.com/mahmoudibrahim/JAMM/wiki/JAMM-Downloads-Archive) or the [Github release page](https://github.com/mahmoudibrahim/JAMM/releases). 
 
@@ -21,7 +21,7 @@ If you are interested in older versions, check the [Downloads Archive](https://g
 Latest News and Updates
 ------
 
-* **Jul 14 2016:** *New version of JAMM released (v1.0.7rev5)*. This version adds -T parameter for custom temporary directory (thanks to @amathelier) as well as streamlined code and fixed bugs in peakfinder.r.
+* **May 17 2019:** *New version of JAMM released (v1.0.7rev6)*. This version features some small changes to input checks.
 
 _Visit the [the Wiki Homepage](https://github.com/mahmoudibrahim/JAMM/wiki) for older updates and news._
 
@@ -35,7 +35,7 @@ JAMM Documentation
  * [JAMM's Output](https://github.com/mahmoudibrahim/JAMM/wiki/JAMM%27s-Output)
  * [Frequently Asked Questions](https://github.com/mahmoudibrahim/JAMM/wiki/Frequently-Asked-Questions)
  * [Parameter Recommendations](https://github.com/mahmoudibrahim/JAMM/wiki/JAMM-Parameter-Recommendation)
- * Of course it is always good to read [the actual paper](http://bioinformatics.oxfordjournals.org/content/31/1/48) :)
+ * Of course it is always good to read [the actual paper](https://academic.oup.com/bioinformatics/article/31/1/48/2365061) :)
 
 Please check [the Wiki Homepage](https://github.com/mahmoudibrahim/JAMM/wiki) for more information on JAMM. 
 
@@ -71,11 +71,10 @@ How to Cite JAMM?
 
 Please cite:
 
-**Ibrahim MM, Lacadie SA, Ohler U (2015). JAMM: A Peak Finder for Joint Analysis of NGS Replicates. _Bioinformatics_, 31(1): 48-55. doi: [10.1093/bioinformatics/btu568] (http://bioinformatics.oxfordjournals.org/content/early/2014/09/15/bioinformatics.btu568)**
+**Ibrahim MM, Lacadie SA, Ohler U (2015). JAMM: A Peak Finder for Joint Analysis of NGS Replicates. _Bioinformatics_, 31(1): 48-55. doi: [10.1093/bioinformatics/btu568] (https://academic.oup.com/bioinformatics/article/31/1/48/23650618)**
 
 
 ---
 
 *Hint: While you run JAMM, you can also go on jammin...*
-
 [![IMAGE ALT TEXT HERE](http://img.youtube.com/vi/HSs1HgM0Wos/0.jpg)](http://www.youtube.com/watch?v=HSs1HgM0Wos)

SignalGenerator.sh

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################
 
 ##Finding out the path
@@ -27,7 +27,7 @@ sPath="`( cd \"$sPath\" && pwd )`"
 usage()
 {
 cat << EOF
-Welcome to JAMM v1.0.7rev5 Signal Generator Script (GNU GPLv3). Copyright (C) 2014-2016  Mahmoud Ibrahim.
+Welcome to JAMM v1.0.7rev5 Signal Generator Script (GNU GPLv3). Copyright (C) 2014-2019  Mahmoud Ibrahim.
 
 This program comes with ABSOLUTELY NO WARRANTY; for details visit http://www.gnu.org/licenses/gpl.html. This is free software, and you are welcome to redistribute it under certain conditions; visit http://www.gnu.org/licenses/gpl.html for details.
 

bincalculator.r

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################
 
 

changelog

@@ -1,6 +1,7 @@
 ===================
-Version 1.0.7rev5
+Version 1.0.7rev6
 ===================
 
-- add -T option to define a custom temporary directory (thanks to Anthony Mathelier[https://github.com/amathelier])
-- streamlined some code parts related to findpeak function and removed a bug there that affected peaks in some extreme parameter/data combinations
+- changed some input checks to make it more compatible with pipeline tools
+- added an input check for -f option
+- updated contact info

peakfilter.pl

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################
 
 

peakfinder.r

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################
 
 

peakhelper.r

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################
 
 

readme

@@ -16,7 +16,7 @@ To install JAMM:
 To get information about options available to JAMM users, run the JAMM bash script without any parameters or visit the documentation page at https://github.com/mahmoudibrahim/JAMM/wiki/Usage
 
 
-If you encounter errors or have questions, please email mahmoud.ibrahim@mdc-berlin.de
+If you encounter errors or have questions, please email mmibrahim@pm.me
 
 
 Important Note: JAMM produces a large number of peaks on purpose to allow you to choose your threshold the way you like. The peaks are scored and ranked by column 7  in the output narrowPeak file. If you want a confident list directly from JAMM, you could use the option "-e auto", although a better way is probably to see the peaks that are reproducible in your replicates.

readshifter.pl

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################
 
 

signalmaker.r

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################
 
 

xcorr.r

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################
 
 

xcorrhelper.r

@@ -1,6 +1,6 @@
 ########################################################################
-# JAMMv1.0.7rev5 is a peak finder for joint analysis of NGS replicates.
-# Copyright (C) 2014-2016  Mahmoud Ibrahim
+# JAMMv1.0.7rev6 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2019  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Contact: mahmoud.ibrahim@mdc-berlin.de
+# Contact: mmibrahim@pm.me
 ########################################################################