[Bioperl-l] BioPerl Google SOC project

[Mark A. Jensen]

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);
>