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.
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Hi there,
is it possible to use wild cards in this statement
ssh $remote_server 'perl -pi -e "s,EXP_SERIAL_19b8be67=\"\",EXP_SERIAL_`hostid`=\"UNKNOWN\"," /var/myfile'
This command works fine but the bit in bold (the 8 character hostid) will not always be 19b8be67 so I was hoping I could... (2 Replies)
Discussion started by: hcclnoodles
2 Replies
2. Shell Programming and Scripting
Is there anyway you can grep using multiple wildcards? When I run the below line the results return fine;
grep 12345 /usr/local/production/soccermatchplus/distributor/clients/*/out/fixtures.xml | awk -F/ '{print $8}'
However ideally, I need it to grep for;
grep 12345... (3 Replies)
Discussion started by: JayC89
3 Replies
3. Shell Programming and Scripting
Good evening All,
I have a perl script to pull out all occurrences of a files beginning with xx and ending in .p. I will then loop through all 1K files in a directory. I can grep for xx*.p files but it gives me the entire line. I wish to output to a single colum with only the hits found. ... (3 Replies)
Discussion started by: CammyD
3 Replies
4. Shell Programming and Scripting
I have a script that runs on one file (at a time).
like this:
$> perl myscript.pl filename > output
How can I run it on >6000 files and have the output sent out into slightly modified file name
$> perl myscript 6000files> output6000files.new extension
Thanks in anticipation (4 Replies)
Discussion started by: aritakum
4 Replies
5. Shell Programming and Scripting
Hi All
I am having hundred over file in the below pattern.
AA050101.INI
BB090101.INI
.
.
ZX980101.INI
Need to rename these files with an extension .bak
AA050101.INI.bak
BB090101.INI.bak
.
.
ZX980101.INI.bak (5 Replies)
Discussion started by: karthikn7974
5 Replies
6. Programming
Hello. This shouldn't be an unusual problem, but I cannot find anything about it at google or at other search machine.
So, I've made an application using C++ and QtCreator. I 've made a new mime type for application's project files.
My system (ubuntu 10.10), when I right click a file and I... (3 Replies)
Discussion started by: hakermania
3 Replies
7. Shell Programming and Scripting
Hi
I have 2 directories t1 and t2 with some files in it. I have to see whether the files present in t1 is also there in t2 or not. Currently, both the directories contain the same files as shown below:
$ABC.TXT
def.txt
Now, when I run the below script, it tells def.txt is found,... (5 Replies)
Discussion started by: guruprasadpr
5 Replies
8. Shell Programming and Scripting
I am dealing will many thousand fairy small files.
I need to search them for various matches and depending on what I find, may need to search some files again for additional matches.
Generally speaking, is it better to write a txt file to an @array/@list and then work with it (multiple... (1 Reply)
Discussion started by: OldGaf
1 Replies
9. Shell Programming and Scripting
Hi,
I want to work with multiple files which all contain 2 numbers.
I tried to make a nested for loop but for some reason it doesn't recognize the $j as a number. The output is cannot open file `175-T-pvalue.xls'. How do I make sure that it takes the numbers from the inner loop as $j?
... (4 Replies)
Discussion started by: linseyr
4 Replies
10. Shell Programming and Scripting
job_count=`grep -e "The job called .* has finished | The job called .* is running" logfile.txt | wc -l`
Any idea how to count those 2 patterns so i have a total count of the finished and running jobs from the log file?
If i do either of the patterns its works okay but adding them together... (8 Replies)
Discussion started by: finn
8 Replies
LEARN ABOUT OSX
apr::perlio
apache_mod_perl-108~358::mod_perl-2.0.7::docs::api::APR:UserlContributed Perl Doapache_mod_perl-108~358::mod_perl-2.0.7::docs::api::APR::PerlIO(3)
NAME
APR::PerlIO -- Perl IO layer for APR
Synopsis
# under mod_perl
use APR::PerlIO ();
sub handler {
my $r = shift;
die "This Perl build doesn't support PerlIO layers"
unless APR::PerlIO::PERLIO_LAYERS_ARE_ENABLED;
open my $fh, ">:APR", $filename, $r->pool or die $!;
# work with $fh as normal $fh
close $fh;
return Apache2::Const::OK;
}
# outside mod_perl
% perl -MAPR -MAPR::PerlIO -MAPR::Pool -le
'open my $fh, ">:APR", "/tmp/apr", APR::Pool->new or die "$!";
print $fh "whoah!";
close $fh;'
Description
"APR::PerlIO" implements a Perl IO layer using APR's file manipulation API internally.
Why do you want to use this? Normally you shouldn't, probably it won't be faster than Perl's default layer. It's only useful when you need
to manipulate a filehandle opened at the APR side, while using Perl.
Normally you won't call open() with APR layer attribute, but some mod_perl functions will return a filehandle which is internally hooked to
APR. But you can use APR Perl IO directly if you want.
Prerequisites
Not every Perl will have full "APR::PerlIO" functionality available.
Before using the Perl IO APR layer one has to check whether it's supported by the used APR/Perl build. Perl 5.8.x or higher with perlio
enabled is required. You can check whether your Perl fits the bill by running:
% perl -V:useperlio
useperlio='define';
It should say define.
If you need to do the checking in the code, there is a special constant provided by "APR::PerlIO", which can be used as follows:
use APR::PerlIO ();
die "This Perl build doesn't support PerlIO layers"
unless APR::PerlIO::PERLIO_LAYERS_ARE_ENABLED;
Notice that loading "APR::PerlIO" won't fail when Perl IO layers aren't available since "APR::PerlIO" provides functionality for Perl
builds not supporting Perl IO layers.
Constants
"APR::PerlIO::PERLIO_LAYERS_ARE_ENABLED"
See Prerequisites.
API
Most of the API is as in normal perl IO with a few nuances listed in the following sections.
META: need to rework the exception mechanism here. Current success in using errno ($!) being set (e.g. on open()) is purely accidental and
not guaranteed across all platforms and functions. So don't rely on $!. Will use "APR::Error" for that purpose.
"open"
Open a file via APR Perl IO layer.
open my $fh, ">:APR", $filename, $r->pool or die $!;
arg1: $fh ( GLOB filehandle )
The filehandle.
arg2: $mode ( string )
The mode to open the file, constructed from two sections separated by the ":" character: the first section is the mode to open the file
under (>, <, etc) and the second section must be a string APR. For more information refer to the open entry in the perlfunc manpage.
arg3: $filename ( string )
The path to the filename to open
arg4: $p ( "APR::Pool" )
The pool object to use to allocate APR::PerlIO layer.
ret: ( integer )
success or failure value (boolean).
since: 2.0.00
"seek"
Sets $fh's position, just like the "seek()" Perl call:
seek($fh, $offset, $whence);
If $offset is zero, "seek()" works normally.
However if $offset is non-zero and Perl has been compiled with with large files support ("-Duselargefiles"), whereas APR wasn't, this
function will croak. This is because largefile size "Off_t" simply cannot fit into a non-largefile size "apr_off_t".
To solve the problem, rebuild Perl with "-Uuselargefiles". Currently there is no way to force APR to build with large files support.
since: 2.0.00
C API
The C API provides functions to convert between Perl IO and APR Perl IO filehandles.
META: document these
See Also
mod_perl 2.0 documentation. The perliol(1), perlapio(1) and perl(1) manpages.
Copyright
mod_perl 2.0 and its core modules are copyrighted under The Apache Software License, Version 2.0.
Authors
The mod_perl development team and numerous contributors.
perl v5.16.2 2011-02-07 apache_mod_perl-108~358::mod_perl-2.0.7::docs::api::APR::PerlIO(3)