how to submit several commands together

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# 1  
how to submit several commands together

Dear all,

I have a simple question. I have many cut commands like below to run. I am wondering how to just type and submit all the commands at once and then each of the command will be run automaticaly one by one. Thanks a lot!

cut -d ' ' -f  3-2002          chr20_step2.mlprob>chr20_part1.mlprob   
cut -d ' ' -f  2003-4002  chr20_step2.mlprob>chr20_part2.mlprob  
cut -d ' ' -f  4003-6002  chr20_step2.mlprob>chr20_part3.mlprob   
cut -d ' ' -f  6003-8002  chr20_step2.mlprob>chr20_part4.mlprob   
cut -d ' ' -f  8003-10002  chr20_step2.mlprob>chr20_part5.mlprob   
cut -d ' ' -f  10003-12002  chr20_step2.mlprob>chr20_part6.mlprob   
cut -d ' ' -f  12003-14002  chr20_step2.mlprob>chr20_part7.mlprob   
cut -d ' ' -f  14003-16002  chr20_step2.mlprob>chr20_part8.mlprob   
cut -d ' ' -f  16003-18002  chr20_step2.mlprob>chr20_part9.mlprob   
cut -d ' ' -f  18003-20002  chr20_step2.mlprob>chr20_part10.mlprob   
cut -d ' ' -f  20003-22002  chr20_step2.mlprob>chr20_part11.mlprob   
cut -d ' ' -f  22003-24002  chr20_step2.mlprob>chr20_part12.mlprob   
cut -d ' ' -f  24003-26002  chr20_step2.mlprob>chr20_part13.mlprob   
cut -d ' ' -f  26003-28002  chr20_step2.mlprob>chr20_part14.mlprob   
cut -d ' ' -f  28003-30002  chr20_step2.mlprob>chr20_part15.mlprob   
cut -d ' ' -f  30003-32002  chr20_step2.mlprob>chr20_part16.mlprob   
cut -d ' ' -f  32003-34002  chr20_step2.mlprob>chr20_part17.mlprob   
cut -d ' ' -f  34003-36002  chr20_step2.mlprob>chr20_part18.mlprob   
cut -d ' ' -f  36003-38002  chr20_step2.mlprob>chr20_part19.mlprob   
cut -d ' ' -f  38003-40002  chr20_step2.mlprob>chr20_part20.mlprob   
cut -d ' ' -f  40003-42002  chr20_step2.mlprob>chr20_part21.mlprob   
cut -d ' ' -f  42003-44002  chr20_step2.mlprob>chr20_part22.mlprob   
cut -d ' ' -f  44003-46002  chr20_step2.mlprob>chr20_part23.mlprob   
cut -d ' ' -f  46003-48002  chr20_step2.mlprob>chr20_part24.mlprob   
cut -d ' ' -f  48003-50002  chr20_step2.mlprob>chr20_part25.mlprob   
cut -d ' ' -f  50003-52002  chr20_step2.mlprob>chr20_part26.mlprob   
cut -d ' ' -f  52003-54002  chr20_step2.mlprob>chr20_part27.mlprob   
cut -d ' ' -f  54003-56002  chr20_step2.mlprob>chr20_part28.mlprob   
cut -d ' ' -f  56003-58002  chr20_step2.mlprob>chr20_part29.mlprob   
cut -d ' ' -f  58003-60002  chr20_step2.mlprob>chr20_part30.mlprob   
cut -d ' ' -f  60003-62002  chr20_step2.mlprob>chr20_part31.mlprob   
cut -d ' ' -f  62003-64002  chr20_step2.mlprob>chr20_part32.mlprob   
cut -d ' ' -f  64003-66002  chr20_step2.mlprob>chr20_part33.mlprob   
cut -d ' ' -f  66003-68002  chr20_step2.mlprob>chr20_part34.mlprob   
cut -d ' ' -f  68003-70002  chr20_step2.mlprob>chr20_part35.mlprob   
cut -d ' ' -f  70003-72002  chr20_step2.mlprob>chr20_part36.mlprob   
cut -d ' ' -f  72003-72518  chr20_step2.mlprob>chr20_part37.mlprob

Last edited by methyl; 04-02-2012 at 08:46 PM.. Reason: please use code tags
# 2  
copy all the commands in a .sh file and execute the sh file


Just at the end of each command put ; and paste the entire text on terminal
# 3  
I am very surprised that these commands work. It is the highest value I have ever seen in a "-f" parameter (but some considerable margin).
What Operating System and version are you running? What Shell do you use?

What size is the file chr20_step2.mlprob?

You can get the commands to execute concurrently within a modern Bourne-type Shell script by suffixing the command with an ampersand & subject to any kernel limitations on the number of processes for an individual user.

cut -d ' ' -f  3-2002 chr20_step2.mlprob>chr20_part1.mlprob &

Hmm. This looks like an attempt to break a non-unix text file into 2000 character chunks, with some characters left over at the end of this extremely long record. Have you considered using the unix command split or dd after dealing with the two-character header?

What are you trying to do?

Last edited by methyl; 04-02-2012 at 09:04 PM..
# 4  
Indeed, you could do:


# Create a file of 3+(2000 * 100) bytes
dd bs=3 count=1 if=/dev/zero > bigfile
dd bs=2000 count=100 if=/dev/zero >> bigfile

exec 5<bigfile

dd bs=3 count=1 of=/dev/null <&5

dd bs=2000 count=1 of=file$N <&5

while [ -s "file$N" ]
  N=`expr $N + 1`
  dd bs=2000 count=1 of=file$N <&5

rm file$N

exec 5<&-

# 5  
If it works it works.. Try:
i=0 ; while [ $((i+=1)) -le 37 ] ; do cut -d ' ' -f $(((i-1)*2000+3))-$((i*2000+2)) chr20_step2.mlprob > chr20_part$i.m1prob; done

Providing there are no more than 72518 columns, otherwise you need to loop until 36 and print the last line separately..

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