[Bioperl-l] BioPerl Google SOC project

[Alok]

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);
>>