[Bioperl-l] BioPerl Google SOC project

[Mark A. Jensen]

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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