Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Shell scripting : pls help me
Top Forums Shell Programming and Scripting Shell scripting : pls help me Post 302460828 by hravisankar on Thursday 7th of October 2010 12:41:22 PM
Old 10-07-2010
Shell scripting problem
My input file (data1) is like this
Chr8:4000-4500
Chr10:4000-4600

I written a shell program like this.
while read LINE;
do echo "$LINE";
samtools faidx Bos_taurusUMD3.fa "$line";
done < data1


It has to read a line like Chr8:4000-4500 from input file and that line has to be executed in a command like 'samtools faidx Bos_taurusUMD3.fa Chr8:4000-4500'. Then I will get the sequence like this.
>Chr8:4000-4500
TAATTCGTTTTTCTTTTTTCCTCTCTGACTCATTTATTTGTACCATTCTATCTTCTAATT
CACTAATCTTATCTTCTGCCTCTGTTATTCTACTATTTGTCGCCTCCAGAGTGTTTTTGA
TCTCATTTATTGCATTATTCATTATATATTGACTCTTTTTTATGTCTTCTAGGTCCTTGT
TAAACCTTTCTTGCATCTTCTCAATCCTTGTCTCCAGGTTATTTATCTGTGATTCCATTT
TGATTTCAAGATTTTGGATCAATTTCACTATCATTATTCAGAATTCTTTATCAGGTAGAT
TCCTTATCTCTTCCTCTTTTGTTTTGTTTGGTGGGCATTTATCCTGTTCCTTTACCTGCT
GGGTATTCCTCTGTCTCTTCATCTTGTTTATATTGCTGAGTTTGGGGTGTCCTTTCTGTA
TTCTGGCAGTTTGTGGAGTTCTCTTTATTGTGGAGTTTCCTCGCTGTGTATGGGTTTGTA
CAGGTGGCTTGTCAAGGTTTC

but when I execute the shell it is displaying the output like this

Chr8:4000-4500
>
Chr10:4000-4600
>
but not displaying the sequence.but I execute the command at $ prompt like
$samtools faidx Bos_taurusUMD3.fa Chr8:4000-4500
it is running and displaying the sequence.

How to execute it in my shell by reading each line from input line, execute it in command and display the sequences.
KINDLY HELP ME
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

scripting guru's pls help me with scripting on AIX

can someone pls help me with the script for a files coming from one system to a particular directory and i want to write a script to move those files to another directory on different system by renaming the files... pls someone help me on this... thanking in anticipation.... (1 Reply)
Discussion started by: thatiprashant
1 Replies

2. Shell Programming and Scripting

difference between AIX shell scripting and Unix shell scripting.

please give the difference between AIX shell scripting and Unix shell scripting. (2 Replies)
Discussion started by: haroonec
2 Replies

3. Shell Programming and Scripting

HELP me PLS... Simple Scripting!

this is my script.... SQL> select * from dba_profiles 2 where resource_name in ('FAILED_LOGIN_ATTEMPTS','PASSWORD_LOCK_TIME') 3 order by profile; and this is the output... PROFILE RESOURCE_NAME RESOURCE... (2 Replies)
Discussion started by: liezer
2 Replies

4. Shell Programming and Scripting

HELP PLS!! Shell Scripting!!

Dear All, forgive me as i am a complete beginner in shell scripting in UNIX. I have a file with data similair to the following 8 McDonalds Sandwich 1.99 9 Mcdonalds Fries 1.20 13 McDonalds Milkshake 1.20 7 ... (9 Replies)
Discussion started by: Mary_xxx
9 Replies

5. Shell Programming and Scripting

hi..all..pls...help..!!..profile scripting..

hi.. I want to customize a user in unix which could have only ftp access and NO TELNET ACCESS! ..... As being a newbie to unix to my understanding the user .profile has to be edited but if someone can explain how to edit it so that i can block telnet access for that user.....Is /etc/profile has... (5 Replies)
Discussion started by: rookie250
5 Replies

6. UNIX for Advanced & Expert Users

pls help me in scripting

i want to write a script that if the time is 8 then it give a message that the time is 8 and if it is 9-10 then it gives a message that time to go to office like that. can any one help me? (3 Replies)
Discussion started by: lakshmananindia
3 Replies

7. Shell Programming and Scripting

shell script, pls help

# for i in `cat oo`;do ls -ld $i;done ls: /var/tmp/i: No such file or directory ls: i: No such file or directory ls: /var/tmp/ii: No such file or directory ls: i: No such file or directory ls: /var/tmp/iii: No such file or directory ls: i: No such file or directory ls: /var/tmp/iiii: No such... (2 Replies)
Discussion started by: cpttak
2 Replies

8. Shell Programming and Scripting

scripting/awk help : awk sum output is not comming in regular format. Pls advise.

Hi Experts, I am adding a column of numbers with awk , however not getting correct output: # awk '{sum+=$1} END {print sum}' datafile 2.15291e+06 How can I getthe output like : 2152910 Thank you.. # awk '{sum+=$1} END {print sum}' datafile 2.15079e+06 (3 Replies)
Discussion started by: rveri
3 Replies

9. Shell Programming and Scripting

Shell program help pls

first queestion if what does "-s" mean? second seqx -n 10000000 -c 10 < $seqfile >$temp seqx? -n? -c? what do these mean? third if && ! cmp -s $missing $temp explain these codes ty (2 Replies)
Discussion started by: imtheone
2 Replies

10. Shell Programming and Scripting

Need help with first shell script pls.

Hi, I'm trying to extract information from one file to update another one and am a bit stuck. the first file is made up of tags e.g. <item>a@b.com</item> jksdhfjkdsh sldkjfds l klsjdf <item> c@d.com </item> what i'd like to do is extract the email addresses between these tags,... (6 Replies)
Discussion started by: newb1000
6 Replies

LEARN ABOUT SUSE

cpanplus::shell

CPANPLUS::Shell(3pm)					 Perl Programmers Reference Guide				      CPANPLUS::Shell(3pm)

NAME

       CPANPLUS::Shell

SYNOPSIS

	   use CPANPLUS::Shell; 	    # load the shell indicated by your
					    # config -- defaults to
					    # CPANPLUS::Shell::Default

	   use CPANPLUS::Shell qw[Classic]  # load CPANPLUS::Shell::Classic;

	   my $ui      = CPANPLUS::Shell->new();
	   my $name    = $ui->which;	    # Find out what shell you loaded

	   $ui->shell;			    # run the ui shell

DESCRIPTION

       This module is the generic loading (and base class) for all "CPANPLUS" shells. Through this module you can load any installed "CPANPLUS"
       shell.

       Just about all the functionality is provided by the shell that you have loaded, and not by this class (which merely functions as a generic
       loading class), so please consult the documentation of your shell of choice.

BUG REPORTS

       Please report bugs or other issues to <bug-cpanplus@rt.cpan.org<gt>.

AUTHOR

       This module by Jos Boumans <kane@cpan.org>.

COPYRIGHT

       The CPAN++ interface (of which this module is a part of) is copyright (c) 2001 - 2007, Jos Boumans <kane@cpan.org>. All rights reserved.

       This library is free software; you may redistribute and/or modify it under the same terms as Perl itself.

SEE ALSO

       CPANPLUS::Shell::Default, CPANPLUS::Shell::Classic, cpanp

perl v5.12.1							    2010-04-26						      CPANPLUS::Shell(3pm)
All times are GMT -4. The time now is 05:17 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy