Can anyone please help me with this code? It gives me below error in linux shell
EDIT: Added full code
./HapView_LDBlock.sh: line 27: syntax error: unexpected end of file
#--------------------------------------------------------------------
#Copyright (c) <2006>, <Chun Zhang and Affymetrix INC.>
#All rights reserved.
#This is OSI certified open source software and is distributed
#under the BSD license.For details please refer to license.txt.
#------------------------------------------------------
#This script is written by Dr. Chun Zhang
#For calculating LD using 4GAM test
#------------------------------------------------------
count=0
chrnum=14
haphead="HapView_Chr"
hapinfo=".info"
happed=".ped"
while [ $count -lt $chrnum ]
do
count=`expr $count + 1`
subcount=0
tmpped=$haphead$count$happed
tmpinfo=$haphead$count$hapinfo
echo $tmpped
echo $tmpinfo
if [ -e $tmpped ]
then
java -jar Haploview.jar -nogui -pedfile $tmpped -info $tmpinfo -dprime -blockoutput GAM
fi
done
Thank you in advance!
3 answers
It seems to me the problem is the ^M (CTRL-M) character at the end of each line. This script was probably written in a text editor in Windows OS and you are trying to run it in Linux. Try to remove those ^M characters and run the script. There are several ways to remove the ^M character.
It's a simple matter of changing line endings. Check this out: http://www.jedit.org/users-guide/line-separators.html
pinku@ram:~/Documents$ ./HapView_LDBlock.sh
./HapView_LDBlock.sh: line 31: syntax error: unexpected end of file
pinku@ram:~/Documents$ cat -te ./HapView_LDBlock.sh
#--------------------------------------------------------------------^M$
#Copyright (c) <2006>, <Chun Zhang and Affymetrix INC.>^M$
#All rights reserved.^M$
#This is OSI certified open source software and is distributed ^M$
#under the BSD license.For details please refer to license.txt. ^M$
#------------------------------------------------------^M$
#This script is written by Dr. Chun Zhang^M$
#For calculating LD using 4GAM test^M$
#------------------------------------------------------^M$
count=0^M$
chrnum=14^M$
haphead="HapView_Chr"^M$
hapinfo=".info"^M$
happed=".ped"^M$
while [ $count -lt $chrnum ]^M$
do^M$
^Icount=`expr $count + 1`^M$
^Isubcount=0^M$
^Itmpped=$haphead$count$happed^M$
^Itmpinfo=$haphead$count$hapinfo^M$
^Iecho $tmpped^M$
^Iecho $tmpinfo^M$
^Iif [ -e $tmpped ] ^M$
^Ithen^M$
^I^I java -jar Haploview.jar -nogui -pedfile $tmpped -info $tmpinfo -dprime -blockoutput GAM ^M$
^Ifi^M$
^Idone^M$
Thank you so much for helping me out on this!
Quick question: Why does the code you pasted for Sam here not correspond to the cat -te output or the code pasted in the question? Please double check your code and give us the exact code you are using.
Also, before the cat -te, your execution points to an error in a non-existent line 31. I'd appreciate it if you could share the file directly with us, using DropBox or some such service. Or let me know if you'd be more comfortable emailing the file to me.
Debug error: There is no 27th line in the given code.
Log in to answer this question.
Your code only contains 18~20 lines. So maybe this is not the full file?
I didn't include all of the comments lines, so...Here is the complete code that was in the file
Thank you!