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Top Forums Shell Programming and Scripting Convert perl program to shell Post 302594989 by balajesuri on Wednesday 1st of February 2012 06:17:10 PM
Old 02-01-2012
Untested.
Code:
#! /bin/bash

while read x
do
    num=`samtools view  110611_s_4.hg18.filtered.sorted.bam $x | wc -l`
    echo -e "$x\t$num" >> 1_4reads.out
done < uniqprobecoordinates.out

But if the file is huge, it should be equally slow (or rather slower) in bash.
This User Gave Thanks to balajesuri For This Post:
 

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LIBBASH(7)							  libbash Manual							LIBBASH(7)

NAME
libbash -- A bash shared libraries package. DESCRIPTION
libbash is a package that enables bash dynamic-like shared libraries. Actually its a tool for managing bash scripts whose functions you may want to load and use in scripts of your own. It contains a 'dynamic loader' for the shared libraries ( ldbash(1)), a configuration tool (ldbashconfig(8)), and some libraries. Using ldbash(1) you are able to load loadable bash libraries, such as getopts(1) and hashstash(1). A bash shared library that can be loaded using ldbash(1) must answer 4 requirments: 1. It must be installed in $LIBBASH_PREFIX/lib/bash (default is /usr/lib/bash). 2. It must contain a line that begins with '#EXPORT='. That line will contain (after the '=') a list of functions that the library exports. I.e. all the function that will be usable after loading that library will be listed in that line. 3. It must contain a line that begins with '#REQUIRE='. That line will contain (after the '=') a list of bash libraries that are required for our library. I.e. every bash library that is in use in our bash library must be listed there. 4. The library must be listed (For more information, see ldbashconfig(8)). Basic guidelines for writing library of your own: 1. Be aware, that your library will be actually sourced. So, basically, it should contain (i.e define) only functions. 2. Try to declare all variables intended for internal use as local. 3. Global variables and functions that are intended for internal use (i.e are not defined in '#EXPORT=') should begin with: __<library_name>_ For example, internal function myfoosort of hashstash library should be named as __hashstash_myfoosort This helps to avoid conflicts in global name space when using libraries that come from different vendors. 4. See html manual for full version of this guide. AUTHORS
Hai Zaar <haizaar@haizaar.com> Gil Ran <ril@ran4.net> SEE ALSO
ldbash(1), ldbashconfig(8), getopts(1), hashstash(1) colors(1) messages(1) urlcoding(1) locks(1) Linux Epoch Linux
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