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Top Forums Shell Programming and Scripting grep/fgrep/egrep for a very large matrix Post 302423089 by realwindfly on Thursday 20th of May 2010 06:43:37 AM
Old 05-20-2010
grep/fgrep/egrep for a very large matrix

All,

I have a problem with grep/fgrep/egrep. Basically I am building a 200 times 200 correlation matrix. The entries of this matrix need to be retrieved from another very large matrix (~100G). I tried to use the grep/fgrep/egrep to locate each entry and put them into one file. It looks very slow with grep/egrep + reg exp. I am thinking that fgrep may will be faster, but not sure.

Does anyone have experience on this topic? or you may suggest some other commands/ways to solve this problem.

Regards,
Gary
 

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GZGREP(1)						      General Commands Manual							 GZGREP(1)

NAME
gzgrep, gzegrep, gzfgrep - search possibly compressed files for a regular expression SYNOPSIS
gzgrep [ grep_options ] [ -e ] pattern filename... DESCRIPTION
gzgrep is used to invoke the grep on compress'ed or gzip'ed files. All options specified are passed directly to grep. If no file is speci- fied, then the standard input is decompressed if necessary and fed to grep. Otherwise the given files are uncompressed if necessary and fed to grep. If gzgrep is invoked as gzegrep or gzfgrep then egrep or fgrep is used instead of grep. If the GREP environment variable is set, gzgrep uses it as the grep program to be invoked. For example: for sh: GREP=fgrep gzgrep string files for csh: (setenv GREP fgrep; gzgrep string files) AUTHOR
Charles Levert (charles@comm.polymtl.ca) SEE ALSO
grep(1), egrep(1), fgrep(1), gzdiff(1), gzmore(1), gznew(1), gzforce(1), gzip(1), gzexe(1) ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +--------------------+-----------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +--------------------+-----------------+ |Availability | SUNWgzip | +--------------------+-----------------+ |Interface Stability | External | +--------------------+-----------------+ NOTES
Source for gzip is available in the SUNWgzipS package. GZGREP(1)
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