[Bioperl-l] BioPerl Google SOC project

Sat Mar 27 03:05:59 UTC 2010

You can also grab the code off the github mirror:

http://github.com/bioperl/bioperl-live

You can either run a checkout, or download the tarball using the 'Download Source' link.  

We'll have an SVN read-only mirror on Google Code as well very soon, if it isn't done already.

chris

On Mar 26, 2010, at 7:08 PM, Mark A. Jensen wrote:

> Hi Alok-- There has been trouble with the code node
> of late. You can get a tarball of all the latest code at
> http://bioperl.org/DIST/nightly_builds/
> Download both bioperl-live and bioperl-run
> cheers,
> MAJ
> ----- Original Message ----- From: "Alok" <watvealo at cse.msu.edu>
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: "BioPerl List" <bioperl-l at bioperl.org>
> Sent: Friday, March 26, 2010 7:06 PM
> Subject: Re: [Bioperl-l] BioPerl Google SOC project
> 
> 
>> Hi Mark,
>> 
>> Thanks a lot for the response. I tried to access the SVN but was unable to do so. My SVN client just times out :-(
>> I even tried SVN links from the BioPerl Wiki (http://www.bioperl.org/wiki/Using_Subversion)
>> But they too are non-responsive.
>> 
>> Thanks,
>> Alok
>> 
>> Mark A. Jensen wrote:
>>> Hi Alok-- Thanks for your interest! You should certainly consider applying. I can work with
>>> you on developing your application. I'm including the bioperl mailing list on this
>>> post; we'll continue to have this conversation on the list so that the helpful, friendly,
>>> knowledgeable, compassionate membership can participate.
>>> WrapperMaker code is currently available in
>>> svn://code.open-bio.org/bioperl/bioperl-dev/trunk/lib/Bio/Tools/WrapperMaker
>>> Probably you want to have a look at Bio::Tools::Run::Samtools in bioperl-run
>>> for an example of how Bio::Tools::Run::WrapperBase and CommandExts are
>>> used (er, by me...).
>>> cheers
>>> MAJ
>>> ----- Original Message ----- From: "Alok" <watvealo at cse.msu.edu>
>>> To: <maj at fortinbras.us>
>>> Sent: Thursday, March 25, 2010 3:23 PM
>>> Subject: BioPerl Google SOC project
>>> 
>>> 
>>>> Hello Mark,
>>>> 
>>>> My name is Alok Watve and I am currently pursuing PhD in Computer
>>>> Science at Michigan State University. I was going through the BioPerl
>>>> Wiki for Google SOC projects. I have good experience with Perl and was
>>>> wondering if I could work on the project "Perl Run Wrappers".
>>>> 
>>>> Prior to joining MSU, I was working with D E Shaw India Software Pvt.
>>>> Ltd. My work was involved in writing Java programs and their perl
>>>> wrappers. We used perl scripts to fire java programs with all the
>>>> correct parameters. So I think I have some idea about what wrappers are.
>>>> However, I have not used BioPerl and may take some time to get familiar
>>>> with the structure. I am fairly confident that I will be able to do this.
>>>> 
>>>> During my work here at MSU. I use perl a lot for doing basic text
>>>> analysis for my projects. Although I rarely use OO features of perl, I
>>>> have used them in past and never had any problems with it. I also
>>>> believe in writing well-documented and user/developer friendly code
>>>> (With comments, command line options for help/documentation).  I have
>>>> attached a simple script I wrote for my project as an example. I have
>>>> also attached my resume for your consideration.
>>>> 
>>>> Please let me know if you think that I am an appropriate candidate and
>>>> whether I should go ahead with submitting an application with BioPerl as
>>>> my Mentor Organization.
>>>> 
>>>> Thanks a lot,
>>>> Alok
>>>> www.cse.msu.edu/~watvealo/
>>>> 
>>> 
>>> 
>>> --------------------------------------------------------------------------------
>>> 
>>> 
>>> 
>>>> #!/usr/bin/perl
>>>> 
>>>> =pod
>>>> 
>>>> =head1 SYNOPSIS
>>>> 
>>>> Script to edit existing box query files to enable random box query.
>>>> This scripts inserts box size on each line corresponding to discrete
>>>> dimension in the existing box query file. The maximum value of "box size"
>>>> depends on the alphabet size.
>>>> 
>>>>   Example
>>>>   ./modify_bqfile.pl -alpha 8 -infile bqfile -outfile mod_bqfile
>>>> 
>>>> Use -perldoc for detailed help on options.
>>>> 
>>>> =head1 OPTIONS
>>>> 
>>>> =over
>>>> 
>>>> =item -infile
>>>> 
>>>> Specifies the name of the input box query file.
>>>> 
>>>> =item -outfile
>>>> 
>>>> Specifies the name of the output file.
>>>> 
>>>> =item -uniform_box
>>>> 
>>>> Specifies size of the uniform box query.
>>>> 
>>>> =item -max_size
>>>> 
>>>> Specifies the maximum box size for random sized box query.
>>>> 
>>>> =item -help
>>>> 
>>>> Displays a brief help message and exits.
>>>> 
>>>> =item -perldoc
>>>> 
>>>> Displays a detailed help.
>>>> 
>>>> =back
>>>> 
>>>> =cut
>>>> 
>>>> use strict;
>>>> use warnings 'all';
>>>> 
>>>> use Getopt::Long;
>>>> use Pod::Usage;
>>>> 
>>>> GetOptions('infile=s' => \my $infile, 'outfile=s' => \my $outfile, 'max_size=i' => \my $maxSize, 'uniform_box=s' => \my $uniformBox,
>>>>          'help' => \my $help, 'perldoc' => \my $perldoc);
>>>> 
>>>> if(defined($perldoc))
>>>> {
>>>>   pod2usage(-verbose => 2);
>>>> }
>>>> 
>>>> if(defined($help))
>>>> {
>>>>   pod2usage(-verbose=> 0);
>>>> }
>>>> 
>>>> if(! (defined($infile) && defined ($outfile) ))
>>>> {
>>>>   die('Please specify input, output files. Use -perldoc
>>>>       for more help');
>>>> }
>>>> 
>>>> # Some basic error checking to ensure script runs ....
>>>> if(!(defined($uniformBox) ||defined($maxSize)))
>>>> {
>>>>   die('Specify either box size for uniform box queries or maximum box size for random box queries');
>>>> }
>>>> 
>>>> # Initialize random number generator.
>>>> srand();
>>>> 
>>>> # Read Input file and find out lines we are interested in
>>>> # Then perfix the line with correct box size as defined by
>>>> # user choice
>>>> open(IN, "<$infile");
>>>> open(OUT, ">$outfile");
>>>> my $count = 0;
>>>> while(my $line = <IN>)
>>>> {
>>>>   if( ($count%64) < 32 )
>>>>   {
>>>>       if(defined($uniformBox))
>>>>       {
>>>>           $line =  sprintf("%d ",$uniformBox) . $line;
>>>>       }
>>>>       elsif(defined($maxSize))
>>>>       {
>>>>           # This line corresponds to the discrete dimension.
>>>>           $line =  sprintf("%d ", int(rand($maxSize))+1  ) . $line;
>>>>       }
>>>>   }
>>>>   $count ++;
>>>>   print OUT $line
>>>> }
>>>> 
>>>> close(OUT);
>>>> close(IN);
>>>> 
>> 
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