[Bioperl-l] bl2seq for many

Aparna Pallavajjala aparna_pall at hotmail.com
Sun May 18 19:07:51 EDT 2008


Hi,
 
does any one know how to run a dos command through perl script?
I am trying to run bl2seq command in a for loop-with the inputs beeing 2 Filehandlers.
 
General syntax of the command is:
 
bl2seq -p programname -i firstfilename -j secondfilename -o
<outputfilenanme>
 
which in my program is :
 
C:\\xxx\\xxx\\xxx\\bl2seq\\bin\\bl2seq -p blastp -i C:\\xxx\\xxx\\xxx\\xx\\FH1  -j C:\\xxx\\xxx\\xxx\\xxx\\FH2  -o C:\\xxx\\xxx\\xxx\\xxx\\FH1.txt");
 
I am trying to call this using system();
 
Please help me.
 
Thanks,
Aparna      
> CC: bioperl-l at lists.open-bio.org> From: cjfields at uiuc.edu> To: aparna_pall at hotmail.com> Subject: Re: [Bioperl-l] bl2seq for many> Date: Fri, 16 May 2008 10:24:31 -0500> > Not sure what you mean here, as bl2seq uses two sequences. From the > bl2seq doc:> "Bl2seq performs a comparison between two sequences using either the > blastn or blastp algorithm. Both sequences must be either nucleotides > or proteins. The options may be obtained by executing 'bl2seq -'."> If you mean running multiple rounds of bl2seq with varying sequences, > the boilerplate demo in the Bio::Tools::Run::StandAloneBlast synopsis > could be modified to do what you want:> > my $factory = Bio::Tools::Run::StandAloneBlast->new(-program => > 'blastp');> # grab two sequences at a time (loop?) and run bl2seq> my $bl2seq_report = $factory->bl2seq($seq1, $seq2);> > Does this answer your question?> > -chris> > On May 16, 2008, at 9:32 AM, Aparna Pallavajjala wrote:> > > Hi,> >> > I would like to know if anyone tried to do bl2seq for multiple > > sequences at a time?> >> > Please let me know how.> >> > Thx,> > Aparna> > _________________________________________________________________> > Keep your kids safer online with Windows Live Family Safety.> > http://www.windowslive.com/family_safety/overview.html?ocid=TXT_TAGLM_WL_Refresh_family_safety_052008> > _______________________________________________> > Bioperl-l mailing list> > Bioperl-l at lists.open-bio.org> > http://lists.open-bio.org/mailman/listinfo/bioperl-l> > Christopher Fields> Postdoctoral Researcher> Lab of Dr. Marie-Claude Hofmann> College of Veterinary Medicine> University of Illinois Urbana-Champaign> > > > 
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