Re: trouble with a regular expresion

Kirk Wythers wrote: On Oct 23, 2008, at 11:09 PM, John W. Krahn wrote: Kirk Wythers wrote: Below is snipit of code that is intended to read in the station_id from the header of each example file. In each case the reg expression is supposed to find the 6 digit number within the parentheses. B

Re: trouble with a regular expresion

Kirk Wythers wrote: Below is snipit of code that is intended to read in the station_id from the header of each example file. In each case the reg expression is supposed to find the 6 digit number within the parentheses. Both files contain 6 lines in the header. For some reason the reg expressio

trouble with a regular expresion

Below is snipit of code that is intended to read in the station_id from the header of each example file. In each case the reg expression is supposed to find the 6 digit number within the parentheses. Both files contain 6 lines in the header. For some reason the reg expression will not catch

Re: perl file parsing

minky arora wrote: > > I have a file of the follwoing form > >> FFM50HR02GMY4E length=75 xy=2604_3772 region=2 run=R_2008_08_19_08_32_31_ > > TCAATGGGTCCGACGGAGAAAGCGCGACAGAAAAGCCCTTTTGT > > TCGACTAGCGTCGTG > >> FFM50HR02F5QTS length=59 xy=2408_2686 region=2 run=R_2008_08_19_08

Re: perl file parsing

Hello, Use bioperl (http://www.bioperl.org/wiki/Main_Page) for this task. This should do what you want: #!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $fastaFile = 'myfile'; my $pattern = 'CTTGGCGAGAAGGGCCGCTACCTGCTGGCCGCCTCCTTCGGCAACGT'; my $blockThreshold = '500'; my $numFasta

Re: Help required in writing a script

Chas. Owens wrote: > On Thu, Oct 23, 2008 at 18:07, Rob Dixon <[EMAIL PROTECTED]> wrote: >> >> Microsoft's 'nmake' is available for free, but some versions have been more >> compatible with standard modules than others, and in any case, as there is >> still >> no C compiler, on its own it is a sol

Re: Help required in writing a script

On Thu, Oct 23, 2008 at 18:07, Rob Dixon <[EMAIL PROTECTED]> wrote: snip > In their endless search for money, Microsoft don't supply a C compiler, > assembler, or linker with any version of Windows in the last twenty years or > so. > Also, because of several deliberate decisions to make people pay

Re: Help required in writing a script

monnappa appaiah wrote: > >i tried to install the "Expect" modulebut i got the below > error msg: [snip] > cpan> install Expect > Running install for module 'Expect' [snip] > Checking if your kit is complete... > Looks good > Warning: prerequisite IO::Pty 1.03 not found. > Warn

Re: Help required in writing a script

On Thu, Oct 23, 2008 at 16:18, monnappa appaiah <[EMAIL PROTECTED]> wrote: snip >i tried to install the "Expect" modulebut i got the below > error msg: snip > ERROR: cannot run the configured compiler 'cl' > (see conf/compilerok.log). Suggestions: > 1) The complier 'cl' is not in yo

Re: Help required in writing a script

Hi, i tried to install the "Expect" modulebut i got the below error msg: cpan> m /Expect/ Going to read C:\Perl\cpan\Metadata Database was generated on Mon, 20 Oct 2008 08:27:31 GMT ModuleBio::MAGE::QuantitationType::ExpectedValue (JASONS/Bio-MAGE-20020902.6 .tar.gz) Module

error while installing the module

Hi all, i tried insalling the module "Expect" but i'm getting the below error msg, can someone help me in installing this module under windows cpan> m /Expect/ Going to read C:\Perl\cpan\Metadata Database was generated on Mon, 20 Oct 2008 08:27:31 GMT ModuleBio::MAGE::Quantitation

Converting Video to FLV

Hi, Does anyone know of a module/library for converting video files to FLV? Thanks Nigel -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] http://learn.perl.org/

Re: Conserving memory

kenTk schreef: > My real application is in logging numerous sets of results each set > saved in > an anonymous array and those arrays referenced from a master array > called @$arrayREFS > When the results are read I clear the data using > @{$arrayREFS[$index]}=(); > but am concerned that Perl's au

perl file parsing

Dear Gurus, I have a file of the follwoing form >FFM50HR02GMY4E length=75 xy=2604_3772 region=2 run=R_2008_08_19_08_32_31_ TCAATGGGTCCGACGGAGAAAGCGCGACAGAAAAGCCCTTTTGT TCGACTAGCGTCGTG >FFM50HR02F5QTS length=59 xy=2408_2686 region=2 run=R_2008_08_19_08_32_31_ AGGACATGCGGCCCGGCG

Re: Help required in writing a script

On Thu, Oct 23, 2008 at 10:49, monnappa appaiah <[EMAIL PROTECTED]> wrote: > i want to run specific commands and the output of those shud be put into a > file. snip So, you will need to learn to use: Net::SSH (if you want to use keys, this is preferable) - http://search.cpan.org/dist/Net-SSH/SSH.

Re: Help required in writing a script

monnappa appaiah wrote: i need help on something i'm working on.I have 127 systems connected in the network, i want to write a script which will run on a management server, i shud be able to connect to each and every system (all the systems have same password) and execute ce

Re: ignore directories with File::Find?

On Wed Oct 22 2008 @ 4:32, protoplasm wrote: > I ran find2perl to give me some output that I included below (in > Sub_directory). If I have no network shares mounted it runs fine. But > I have some shares mounted (sftp, or smb, etc.) via Nautilus, the > below script really takes a long time. It be

Re: Help required in writing a script

i want to run specific commands and the output of those shud be put into a file. On Thu, Oct 23, 2008 at 8:13 PM, Chas. Owens <[EMAIL PROTECTED]> wrote: > On Thu, Oct 23, 2008 at 10:34, monnappa appaiah <[EMAIL PROTECTED]> > wrote: > > Hi, > > i connect to machines using ssh, i need to co

Re: Help required in writing a script

On Thu, Oct 23, 2008 at 10:34, monnappa appaiah <[EMAIL PROTECTED]> wrote: > Hi, > i connect to machines using ssh, i need to collect only > stdout..connecting to all those machines serially or parllely is fine. > > Thanks, > Monnappa snip Do you want to run arbitrary commands at any tim

Re: Help required in writing a script

Hi, i connect to machines using ssh, i need to collect only stdout..connecting to all those machines serially or parllely is fine. Thanks, Monnappa On Thu, Oct 23, 2008 at 7:50 PM, Chas. Owens <[EMAIL PROTECTED]> wrote: > On Thu, Oct 23, 2008 at 09:36, monnappa appaiah <[EMAIL PROTE

Re: Help required in writing a script

On Thu, Oct 23, 2008 at 09:36, monnappa appaiah <[EMAIL PROTECTED]> wrote: > Hi all, > > i need help on something i'm working on.I have 127 > systems connected in the network, i want to write a script which will run on > a management server, i shud be able to connect to each an

get list of accessible directories

Hello, on our linux system I have a script that runs as root that should return a list of subdirectorys a specific user can access. I have the four directories and aside the users that can access them dira ( usera,userb, userc) dirb ( userb ) dirc ( userc ) dird ( usera, userc ) When

Re: Conserving memory

On Wed, Oct 22, 2008 at 16:25, kenTk <[EMAIL PROTECTED]> wrote: snip > Thanks. > My real application is in logging numerous sets of results each set > saved in > an anonymous array and those arrays referenced from a master array > called @$arrayREFS > When the results are read I clear the data usin

Re: Help required in writing a script

Look at Net::SSH. On Thu, Oct 23, 2008 at 9:36 AM, monnappa appaiah <[EMAIL PROTECTED]>wrote: > Hi all, > > i need help on something i'm working on.I have 127 > systems connected in the network, i want to write a script which will run > on > a management server, i shud be abl

Help required in writing a script

Hi all, i need help on something i'm working on.I have 127 systems connected in the network, i want to write a script which will run on a management server, i shud be able to connect to each and every system (all the systems have same password) and execute certain commands an

RE: Reading from multiple sockets.

Kammen van, Marco, Springer SBM NL wrote: > >>> From: Peter Scott [mailto:[EMAIL PROTECTED] >>> Subject: Re: Reading from multiple sockets. > >> On Tue, 21 Oct 2008 12:53:53 +0200, Kammen van, Marco, Springer SBM NL >> wrote: >> I'm pretty new to working with sockets in perl, looked around for

Re: Conditional replace

John W. Krahn wrote: Brian wrote: Partial success. The value is normally located starting at the 35th char into the line. I split the line so it was at the beginning of a new line and with> worked. Unfortunately the dates never changed. I will sleep on this and attack it again in the mornin

Re: ignore directories with File::Find?

protoplasm wrote: I ran find2perl to give me some output that I included below (in Sub_directory). If I have no network shares mounted it runs fine. But I have some shares mounted (sftp, or smb, etc.) via Nautilus, the below script really takes a long time. It begins to search through ~/.gvfs whi

RE: Reading from multiple sockets.

-Original Message- From: John W. Krahn [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 22, 2008 2:51 PM To: Perl Beginners Subject: Re: Reading from multiple sockets. Kammen van, Marco, Springer SBM NL wrote: > >>> From: Peter Scott [mailto:[EMAIL PROTECTED] >>> Subject: Re: Readin

ignore directories with File::Find?

I ran find2perl to give me some output that I included below (in Sub_directory). If I have no network shares mounted it runs fine. But I have some shares mounted (sftp, or smb, etc.) via Nautilus, the below script really takes a long time. It begins to search through ~/.gvfs which is where Nautilus

Re: Conserving memory

On Oct 21, 10:14 pm, [EMAIL PROTECTED] (Dr.Ruud) wrote: > "Mr. Shawn H. Corey" schreef: > > > > > kenTk: > >> If I populate @array > >> Then > >> @array=(); > >> Is the memory that was used for that array now freed? > > > Yes, providing no other variable contains those items.  For example: > > > my

Re: using unix command issue...

On Oct 21, 4:40 am, [EMAIL PROTECTED] (John W. Krahn) wrote: > Ariel Casas wrote: > > Hello all, > > Hello, > > > > > Any time I run a unix command where I initiate a variable > use the > > variable as an arg in the unix command > pipe it to another unix > > command, I get an error.  This is the er

Re: expect error

On Oct 21, 8:27 pm, [EMAIL PROTECTED] (Juan Pablo Feria Gomez) wrote: > > use strict; > > use warnings; > > use Expect; > > use IO::Tty; > > > $host = "192.168.1.72"; > > $passwd= "xyz"; > > $user = "xyz"; > > > $t= "file.txt"; > > my $connect = Expect->spawn("scp $t [EMAIL PROTECTED]:/work/$user/"