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Top Forums Shell Programming and Scripting Convert perl program to shell Post 302594976 by bhargavpbk88 on Wednesday 1st of February 2012 04:57:30 PM
Old 02-01-2012
this is a command in bash using samtools package
samtools view 110611_s_4.hg18.filtered.sorted.bam chr3:22937492-3299833 | wc -l

this gives me output like a number 8
i want output file like
chr3:22937492-3299833 8

And the input file has many rows having chromosome information for each chromosome i want output and corresponding number from command i mentioned in the top.
i tried in perl but its taking very long time as the files are very huge.

Thanks.
 

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RBASH(1)						      General Commands Manual							  RBASH(1)

NAME
rbash - restricted bash, see bash(1) RESTRICTED SHELL
If bash is started with the name rbash, or the -r option is supplied at invocation, the shell becomes restricted. A restricted shell is used to set up an environment more controlled than the standard shell. It behaves identically to bash with the exception that the follow- ing are disallowed or not performed: o changing directories with cd o setting or unsetting the values of SHELL, PATH, ENV, or BASH_ENV o specifying command names containing / o specifying a file name containing a / as an argument to the . builtin command o specifying a filename containing a slash as an argument to the -p option to the hash builtin command o importing function definitions from the shell environment at startup o parsing the value of SHELLOPTS from the shell environment at startup o redirecting output using the >, >|, <>, >&, &>, and >> redirection operators o using the exec builtin command to replace the shell with another command o adding or deleting builtin commands with the -f and -d options to the enable builtin command o using the enable builtin command to enable disabled shell builtins o specifying the -p option to the command builtin command o turning off restricted mode with set +r or set +o restricted. These restrictions are enforced after any startup files are read. When a command that is found to be a shell script is executed, rbash turns off any restrictions in the shell spawned to execute the script. SEE ALSO
bash(1) GNU Bash-4.0 2004 Apr 20 RBASH(1)
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