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)