bamPlotExample.sh

#!/usr/bin/bash
cd /home/cl512/pipeline/

# The MIT License (MIT)

# Copyright (c) 2013 Charles Lin

# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:

# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.

# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.

#bamPlot.py makes publication quality tracks of ChIP-Seq data that can be edited in adobe illustrator


#HOW TO USE: 

#1. Make a copy of this script and rename it for each job.
#2. Edit variables in the parameters
#3. cd to folder containing script
#4. run by typing 'bash ./script.sh where script.sh is the name of your script


#====================================================
#====================PARAMETERS======================
#====================================================

#replace BAM1,BAM2 with file paths of sorted bam files
#can add BAM3 and NAME3  etc... using same convention

BAM1='sample1.sorted.bam'
BAM2='sample2.sorted.bam'

#Edit the names to give each bam a title
NAME1='sample1'
NAME2='sample2'

#edit these variables to specify region, genome, title etc...
REGION='chr1:+:1001000-1002000'  
GENOME='HG18'
OUTPUT='OUTPUTFOLDER'
TITLE='TITLE'
YAXIS='UNIFORM'    #use either UNIFORM or RELATIVE
SENSE='both' #sense of reads plotted. use either 
COLOR='255,0,0:0,0,255' #use a colon separated list of RGB colors w/ values from 0 to 255


echo
echo Using $BAM1 as BAM1
echo Using $BAM1 as BAM1
echo Calling bamPlot.py on region $REGION in genome $GENOME and directing output to $TITLE in $OUTPUT
echo
echo Running the following command:
#COMMAND
echo python bamPlot.py -b $BAM1,$BAM2 -i $REGION -t $TITLE -y UNIFORM -o $OUTPUT -n $NAME1,$NAME2 -p single -c $COLOR -s $SENSE
python bamPlot.py -b $BAM1,$BAM2 -i $REGION -t $TITLE -y UNIFORM -o $OUTPUT -n $NAME1,$NAME2 -p single -c $COLOR -s $SENSE