From alexeymorozov1991 at gmail.com  Wed Oct  1 01:12:59 2014
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Wed, 1 Oct 2014 10:12:59 +0900
Subject: [Bioperl-l] Getting pairwise alignment scores for existing
 multiple alignment
In-Reply-To: <C9F90635-0BC1-4F41-93FD-13A2897AE023@illinois.edu>
References: <CAK=7cMOkPqofM6j12X77kBFhUb6ZPNFXNeN3YEHsQZU1r+yeDg@mail.gmail.com>
	<C9F90635-0BC1-4F41-93FD-13A2897AE023@illinois.edu>
Message-ID: <CAK=7cMMwgUwoAsLjY5gTnNMNKMKCMqUtNnc1Pauja3eHCrBkHg@mail.gmail.com>

Thanks Chris,
the module you mentioned can only calculate score for nucleic acids, and I
am in fact working with aminoacids alignment. However, I've written the sub
for my needs (it's below, in case someone else needs it).

sub score_aln
        {
        #Takes two alignment lines AS STRINGS;
        #Assumes $matrix (Bio::Matrix::Generic), $open_penalty and
$extend_penalty to be declared as global variables

        die "Different lengths of sequences:\n$_[0]\n$_[1]\n" if
length$_[0]!=length$_[1];
        my @line1=split(//,$_[0]);
        my @line2=split(//,$_[0]);
        my $score=0;
        my $extend=0;
        #Below we count score for each pair (two AA, new gap or gap
extension)
        CHAR:for (my $j=0;$j<scalar(@line1);$j++)
                {
                if (($line1[$j] eq '-')or($line2[$j] eq '-'))
                        {
                        next CHAR if ($line1[$j] eq $line2[$j]);
                        #Skip positions with both sequences containing gaps
(in case we haven't filtered them before)
                        if ($extend==0)
                                {
                                $score-=$open_penalty;
                                $extend=1;
                                }
                        else {$score-=$extend_penalty;}
                        }
                else
                        {
                        $score+=$matrix->get_entry($line1[$j],$line2[$j]);
                        $extend=0;
                        }
                }
        return $score;
        }


2014-10-01 1:54 GMT+09:00 Fields, Christopher J <cjfields at illinois.edu>:

>  On Sep 30, 2014, at 1:20 AM, Alexey Morozov <alexeymorozov1991 at gmail.com>
> wrote:
>
>  Dear colleagues,
>  Is there a method in bioperl that will calculate pairwise alignment
> scores for any given pair of genes in MSA (according to a given matrix and
> gap opening/extension cost)? It seems that Bio::SimpleAlign methods only
> work with score if it has been described in MSA file and can only hold a
> general multiple sequence alignment score.
>
> --
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
>
>
>  Bio::Align::PairwiseStatistics appears to deal with this, see if it fits
> your needs.  You may need to extract the pairwise alignment of the two
> genes if they are in a multiple sequence alignment.
>
>  chris
>
>


-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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From andreas at sdsc.edu  Tue Oct  7 18:52:07 2014
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 7 Oct 2014 11:52:07 -0700
Subject: [Bioperl-l] The NIH Software Discovery Index | We invite your
 comments -- a system for linking software,
 publications and users in the research community.
Message-ID: <CALthepx6CL6tPDWrfz2-UFLtYAUCOsP9_djPoAE4jZtCvdvacg@mail.gmail.com>

Greetings Everyone,



On behalf of a number of software developers, end-users, publishers
associated with the scientific analysis community, we would like to invite
all of you to review a document generated as a result of a NIH BD2K
supported meeting that focused on the opportunities and challenges of
developing a software management ecosystem that could be valuable for
finding and linking software, publications and users in the research
community. You may be also be aware of a related project, the Data
Discovery Index, which will be fully integrated with the software system.

The product of this workshop and the subsequent discussion is a document
which details the opportunities and challenges of developing a Software
Discovery Index that would enable researchers to find, cite, and link
software and analysis tools publications and researchers. To ensure that
the opportunities, challenges, and recommendations detailed in the document
reflect the breadth of experience from the community, we are seeking your
input.  In conjunction with related efforts already under way at NIH,
including the development of a Data Discovery Index, the final document
will be used by the NIH Office of the Associate Director (ADDS) to inform a
strategy for the development of a Software Discovery Index and a commons
ecosystem for data, software, and resources.



We need your help to ensure that this critical task is achieved: to guide
the development of a community based system that gives credit and
acknowledgment to the builder and maintainers of the software we all depend
on! We invite all users, software developers, publishers, and software
repository administrators to review our report prior to its submission to
the NIH. Please complete your review and post comments by November 1, 2014.



The link to the report is here: http://softwarediscoveryindex.org



On behalf of the organizing committee, thank you for your assistance!



Organizing Committee



Owen White

Director of Bioinformatics, University of Maryland, Baltimore, School of
Medicine

Co-Chair of NIH BD2K  Software Index Workshop



Asif Dhar

Principal & Chief Medical Informatics Officer

Co-Chair of NIH BD2K  Software Index Workshop



Vivien Bonazzi

Senior Advisor for Data Science Technologies (ADDS)

Co-Chair of BD2K Software and Methods Group



Jennifer Couch

Chief, Structural Biology and Molecular Applications Branch

NCI Co-Chair of BD2K Software and Methods Group



Chris Wellington

Program Director (NHGRI)
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From cacaucenturion2 at gmail.com  Fri Oct 10 17:46:55 2014
From: cacaucenturion2 at gmail.com (Cacau Centurion)
Date: Fri, 10 Oct 2014 10:46:55 -0700
Subject: [Bioperl-l] Problems when using PAML::yn00
Message-ID: <CA+SvvBWqAhZSb8kqbXx=QLDsVPMMuvMuf5y+U==ttBc9u11hxw@mail.gmail.com>

Hi All,

I tried to use PAML:Yn00 to run yn00 and parse the result. However, no
results were given. Does anyone know what might be the problem?

The following code is obtained from
http://search.cpan.org/dist/BioPerl-Run/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm

use Bio::Tools::Run::Phylo::PAML::Yn00;
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(
    -format => 'fasta',
    -file   => "$ARGV[0]"
);
my $aln = $alignio->next_aln;

my $yn = Bio::Tools::Run::Phylo::PAML::Yn00->new();
$yn->alignment($aln);
my ( $rc, $parser ) = $yn->run;
while ( my $result = $parser->next_result ) {
    my @otus     = $result->get_seqs();
    my $MLmatrix = $result->get_MLmatrix();

    #0 and 1 correspond to the 1st and 2nd entry in the @otus array
    my $dN   = $MLmatrix->[0]->[1]->{dN};
    my $dS   = $MLmatrix->[0]->[1]->{dS};
    my $kaks = $MLmatrix->[0]->[1]->{omega};
    print "Ka = $dN Ks = $dS Ka/Ks = $kaks\n";
}


###########################################################
Alignment:
>1
aaattgttgttg
>2
aacaatttgttg


Yours,
Cacau
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From daniel.lang at biologie.uni-freiburg.de  Wed Oct 15 09:03:55 2014
From: daniel.lang at biologie.uni-freiburg.de (Daniel Lang)
Date: Wed, 15 Oct 2014 11:03:55 +0200
Subject: [Bioperl-l] Parent/parent_id attribute
In-Reply-To: <892AC2D6-99CA-42EB-9EF8-7496C7D6F670@illinois.edu>
References: <542066E5.5060401@biologie.uni-freiburg.de>
	<892AC2D6-99CA-42EB-9EF8-7496C7D6F670@illinois.edu>
Message-ID: <543E387B.3030907@biologie.uni-freiburg.de>

Hi Chris,

thanks for you response! No, there hasn't been a response yet.

The solution with add_tag_value('Parent') works for me tough.

Best,
Daniel

On 28.09.2014 05:26, Fields, Christopher J wrote:
> Hi Daniel,
> 
> Not sure if you got an answer to this one yet.  I?m cc?ing the gmod-gbrowse group just in case this was missed here.  
> 
> chris
> 
> On Sep 22, 2014, at 1:13 PM, Daniel Lang <Daniel.Lang at biologie.uni-freiburg.de> wrote:
> 
>> Hi,
>>
>> I'm using bioperl 1.6.923-1 (Ubuntu Trusty package) and
>> Bio::DB::SeqFeature to store and manipulate GFF3 files.
>>
>> I'm wondering why the "Parent" GFF3 attributes are stored as parent_id
>> values in the feature objects, but not returned as such in the gff3_string?
>>
>> GFF3:
>> Chr01   transdecoder    mRNA    5216    5627    .       +       .
>> ID=T1.Chr01.mRNA.1;Parent=T1.Chr01.gene.1;Alias=T1.asmbl_1|m.6484,T1.ORF;Name=T1.Chr01.mRNA.1
>>
>> Example debugger trace after fetching stored feature:
>>
>> x $f
>> 0  Bio::DB::SeqFeature=HASH(0x3e3a798)
>>   'attributes' => HASH(0x3e3a858)
>>      'Alias' => ARRAY(0x3e3a8b8)
>>         0  'T1.asmbl_1|m.6484'
>>         1  'T1.ORF'
>>      'load_id' => ARRAY(0x3e3aca8)
>>         0  'T1.Chr01.mRNA.1'
>>      'parent_id' => ARRAY(0x3e3acf0)
>>         0  'T1.Chr01.gene.1'
>>   'is_circular' => 0
>>   'name' => 'T1.Chr01.mRNA.1'
>>   'phase' => undef
>>   'primary_id' => 2428
>>   'ref' => 'Chr01'
>>   'score' => undef
>>   'source' => 'transdecoder'
>>   'start' => 5216
>>   'stop' => 5627
>>   'store' => Bio::DB::SeqFeature::Store::DBI::mysql=HASH(0x39b95d0)
>>      'class_loaded' => HASH(0x3e3a2b8)
>>         'Bio::DB::SeqFeature' => 1
>>      'dbh' => DBI::db=HASH(0x3dc1e40)
>>           empty hash
>>      'dumpdir' => '/tmp'
>>      'is_temp' => undef
>>      'namespace' => undef
>>      'seqfeatureclass' => 'Bio::DB::SeqFeature'
>>      'settings_cache' => HASH(0x3dc1d98)
>>         'autoindex' => 1
>>         'compress' => 0
>>         'index_subfeatures' => 1
>>         'serializer' => 'Storable'
>>      'writeable' => undef
>>   'strand' => 1
>>   'type' => 'mRNA'
>>
>> x $f->gff3_string
>> 0
>> "Chr01\cItransdecoder\cImRNA\cI5216\cI5627\cI.\cI+\cI.\cIName=T1.Chr01.mRNA.1;ID=2428;Alias=T1.asmbl_1%7Cm.6484,T1.ORF"
>>
>> What is the best practice to store parentage? I'm currently adding an
>> additional "Parent" value using add_tag_value.
>>
>> Or is this a bug in the version I'm using?
>>
>> Best,
>> Daniel
>> -- 
>>
>> Dr. Daniel Lang
>> University of Freiburg, Plant Biotechnology
>> Schaenzlestr. 1, D-79104 Freiburg
>> fax:        +49 761 203 6945
>> phone:      +49 761 203 6989
>> homepage:   http://www.plant-biotech.net/
>>            http://www.cosmoss.org/
>> e-mail:     daniel.lang at biologie.uni-freiburg.de
>>
>> #################################################
>> My software never has bugs.
>> It just develops random features.
>> #################################################
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
> 






From cjfields at illinois.edu  Wed Oct 15 15:12:28 2014
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 15 Oct 2014 15:12:28 +0000
Subject: [Bioperl-l] Parent/parent_id attribute
In-Reply-To: <543E387B.3030907@biologie.uni-freiburg.de>
References: <542066E5.5060401@biologie.uni-freiburg.de>
	<892AC2D6-99CA-42EB-9EF8-7496C7D6F670@illinois.edu>
	<543E387B.3030907@biologie.uni-freiburg.de>
Message-ID: <481FA2ED-9AC6-4860-AAD9-88767252EE3D@illinois.edu>

It?s been a little quiet lately :)

chris

On Oct 15, 2014, at 4:03 AM, Daniel Lang <Daniel.Lang at biologie.uni-freiburg.de> wrote:

> Hi Chris,
> 
> thanks for you response! No, there hasn't been a response yet.
> 
> The solution with add_tag_value('Parent') works for me tough.
> 
> Best,
> Daniel
> 
> On 28.09.2014 05:26, Fields, Christopher J wrote:
>> Hi Daniel,
>> 
>> Not sure if you got an answer to this one yet.  I?m cc?ing the gmod-gbrowse group just in case this was missed here.  
>> 
>> chris
>> 
>> On Sep 22, 2014, at 1:13 PM, Daniel Lang <Daniel.Lang at biologie.uni-freiburg.de> wrote:
>> 
>>> Hi,
>>> 
>>> I'm using bioperl 1.6.923-1 (Ubuntu Trusty package) and
>>> Bio::DB::SeqFeature to store and manipulate GFF3 files.
>>> 
>>> I'm wondering why the "Parent" GFF3 attributes are stored as parent_id
>>> values in the feature objects, but not returned as such in the gff3_string?
>>> 
>>> GFF3:
>>> Chr01   transdecoder    mRNA    5216    5627    .       +       .
>>> ID=T1.Chr01.mRNA.1;Parent=T1.Chr01.gene.1;Alias=T1.asmbl_1|m.6484,T1.ORF;Name=T1.Chr01.mRNA.1
>>> 
>>> Example debugger trace after fetching stored feature:
>>> 
>>> x $f
>>> 0  Bio::DB::SeqFeature=HASH(0x3e3a798)
>>>  'attributes' => HASH(0x3e3a858)
>>>     'Alias' => ARRAY(0x3e3a8b8)
>>>        0  'T1.asmbl_1|m.6484'
>>>        1  'T1.ORF'
>>>     'load_id' => ARRAY(0x3e3aca8)
>>>        0  'T1.Chr01.mRNA.1'
>>>     'parent_id' => ARRAY(0x3e3acf0)
>>>        0  'T1.Chr01.gene.1'
>>>  'is_circular' => 0
>>>  'name' => 'T1.Chr01.mRNA.1'
>>>  'phase' => undef
>>>  'primary_id' => 2428
>>>  'ref' => 'Chr01'
>>>  'score' => undef
>>>  'source' => 'transdecoder'
>>>  'start' => 5216
>>>  'stop' => 5627
>>>  'store' => Bio::DB::SeqFeature::Store::DBI::mysql=HASH(0x39b95d0)
>>>     'class_loaded' => HASH(0x3e3a2b8)
>>>        'Bio::DB::SeqFeature' => 1
>>>     'dbh' => DBI::db=HASH(0x3dc1e40)
>>>          empty hash
>>>     'dumpdir' => '/tmp'
>>>     'is_temp' => undef
>>>     'namespace' => undef
>>>     'seqfeatureclass' => 'Bio::DB::SeqFeature'
>>>     'settings_cache' => HASH(0x3dc1d98)
>>>        'autoindex' => 1
>>>        'compress' => 0
>>>        'index_subfeatures' => 1
>>>        'serializer' => 'Storable'
>>>     'writeable' => undef
>>>  'strand' => 1
>>>  'type' => 'mRNA'
>>> 
>>> x $f->gff3_string
>>> 0
>>> "Chr01\cItransdecoder\cImRNA\cI5216\cI5627\cI.\cI+\cI.\cIName=T1.Chr01.mRNA.1;ID=2428;Alias=T1.asmbl_1%7Cm.6484,T1.ORF"
>>> 
>>> What is the best practice to store parentage? I'm currently adding an
>>> additional "Parent" value using add_tag_value.
>>> 
>>> Or is this a bug in the version I'm using?
>>> 
>>> Best,
>>> Daniel
>>> -- 
>>> 
>>> Dr. Daniel Lang
>>> University of Freiburg, Plant Biotechnology
>>> Schaenzlestr. 1, D-79104 Freiburg
>>> fax:        +49 761 203 6945
>>> phone:      +49 761 203 6989
>>> homepage:   http://www.plant-biotech.net/
>>>           http://www.cosmoss.org/
>>> e-mail:     daniel.lang at biologie.uni-freiburg.de
>>> 
>>> #################################################
>>> My software never has bugs.
>>> It just develops random features.
>>> #################################################
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> 
>