06-11-2010
Quote:
Originally Posted by
japaneseguitars
i have a file that contains information about genes and I need to obtain the sequences upstream and downstream these genes and do analysis on that. These 19 files are the chromosome sequences. I have sorted the gene file based on chromosome location so I can essentially use 1 chromosome file at a time since I just tried to open all of them and perl ran out of memory =/
So why do all 19 files need to be open if you are processing 1 file at a time?
Do you have simple logic and maybe the Perl experts here can help? ie, present pseudo code of what you want to do, size of files, output desired, intermediate processing needed, platform.
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LEARN ABOUT REDHAT
filecache
FileCache(3pm) Perl Programmers Reference Guide FileCache(3pm)
NAME
FileCache - keep more files open than the system permits
SYNOPSIS
use FileCache;
# or
use FileCache maxopen => 16;
cacheout $path;
print $path @data;
cacheout $mode, $path;
print $path @data;
DESCRIPTION
The "cacheout" function will make sure that there's a filehandle open for reading or writing available as the pathname you give it. It
automatically closes and re-opens files if you exceed your system's maximum number of file descriptors, or the suggested maximum.
cacheout EXPR
The 1-argument form of cacheout will open a file for writing ('>') on it's first use, and appending ('>>') thereafter.
cacheout MODE, EXPR
The 2-argument form of cacheout will use the supplied mode for the initial and subsequent openings. Most valid modes for 3-argument
"open" are supported namely; '>', '+>', '<', '<+', '>>', '|-' and '-|'
CAVEATS
If you use cacheout with '|-' or '-|' you should catch SIGPIPE and explicitly close the filehandle., when it is closed from the other end
some cleanup needs to be done.
While it is permissible to "close" a FileCache managed file, do not do so if you are calling "FileCache::cacheout" from a package other
than which it was imported, or with another module which overrides "close". If you must, use "FileCache::cacheout_close".
BUGS
sys/param.h lies with its "NOFILE" define on some systems, so you may have to set maxopen ($FileCache::cacheout_maxopen) yourself.
perl v5.8.0 2002-06-01 FileCache(3pm)