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Amin Momin | 9 Feb 22:23
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parsing swissprot using SeqIO::swiss


Hi

I am trying to parse the swissprot text files to capture the feature (FT) information. However I cant find
any documentation to get the information from the functions _print_swissprot_FTHelper and
_read_swissprot_FTHelper that capture the feature table. Can someone give any suggestions.

Thanks,
 Amin
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Fields, Christopher J | 8 Feb 20:24
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bioperl-guts filtering

Just noticed a huge backlog of spam as well as lots of github commits caught up on the bioperl-guts-l
listserv.  There is also some buildbot stuff coming in, we need to change the sender to something other than
bioperl-guts-l (spoofing the sender to be the same as the recipient is a common spam mechanism).

I am setting the default non-member to simply reject incoming email for that list and to hold member posts,
along with a message to post bioperl questions to bioperl-l.  Any complaints on that?  Seems like we should
be keeping the posts to automated stuff anyway…

chris
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Adam Sjøgren | 8 Feb 13:28
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Memory leak in Bio::SeqIO::staden::read->staden_read_trace() ?

  Hi.

I am using Bio::SeqIO(staden::read) to read .ab1 files in a long lived
(daemon) process, and I have noticed that memory usage keeps growing
somewhat rapidly.

I have thrown together a small script that illustrates what I am seeing:

#!/usr/bin/perl

# test.pl - illustrate possible memory leak in Bio::SeqIO::staden::read->staden_read_trace
#           Example .ab1 file found via first hit on Google: http://www.elimbio.com/Forms/pGEM.zip

use strict;
use warnings;

use Bio::SeqIO;

while (1) {
    print "Reading 100 times\n";
    for my $i (1 .. 100) {
        my $in=Bio::SeqIO->new(-file=>'pGEM_(ABI)_A01.ab1', -format=>'abi');
        my $seq=$in->next_seq(); # This seems to leak memory
    }
    print "Sleeping\n";
    sleep 5;
}

Running this, and running 'while (( 1 )); do ps fauxww | grep [t]est.pl;
sleep 2; done;' I see an increase of memory usage by ~30MB per 100 read
(Continue reading)

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Casandra | 7 Feb 17:11
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help!

Hi,

I'm trying to install Bioperl but I'm a bit lost. I know I have perl  
installed becaused I have already write some scripts but I'm biologist  
so... not pretty sure about what messages say.

My perl version:
This is perl, v5.8.8 built for darwin-thread-multi-2level
My computer:
Mac OS X Vesion 10.5.8

I was following this preliminary steps:

--------------
PRELIMINARY PREPARATION

    This is optional, but regardless of your subsequent choice of
    installation method, it will help to carry out the following steps.
    They will increase the likelyhood of installation success
    (especially of optional dependencies).

      * Upgrade CPAN:

  >perl -MCPAN -e shell
  cpan>install Bundle::CPAN
  cpan>q				

      * Install/upgrade Module::Build, and make it your preferred
        installer:
(Continue reading)

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Em Rich | 6 Feb 17:09
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Embedding hyperlinks in SVG files

Hi,

I am currently using Bio::Graphics to render sequence images into SVG
format. As SVGs can inherently embed hyperlinks using the xlink
attribute I was wondering if there is a straight forward way of adding
this attribute type in Bio::Graphics rather than creating an image
map.

Thanks,

Emily
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DANIEL EDUARDO TORRENTE QUINTERO | 5 Feb 20:04
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Bioperl parsing output file

i need some help in this script

#!/usr/bin/perl
use Bio::SearchIO;

$report_obj = new Bio::SearchIO(-format => 'blast',
                     -file   => 'C:\blast-2.2.25+\Lib3_consensus_dbAt.xml');
    while( $result = $report_obj->next_result ) {
        while( $hit = $result->next_hit ) {
           while( $hsp = $hit->next_hsp ) {
              if ( $hsp->evalue <= 0.00001 ) {
                   print "Hit\t", $hit->name, "\n", "Length\t", $hsp->length('total'),
                   "\n", "Percent_id\t",
                   $hsp->percent_identity, "\n",$result>query_name(),;  }  } } }

I want to export the results of de perl script on a file but i dont know how..... i tried to use all the 
Bio::SearchIO::Writer<http://www.bioperl.org/wiki/Module:Bio::SearchIO::Writer> methods but
i cant make it work with this script.
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Puneet Kadimi | 2 Feb 04:18
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Check out my photos on Facebook

Hi Bioperl-l,

I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so
you can see it. First, you need to join Facebook! Once you join, you can also create your own profile.

Thanks,
Puneet

To sign up for Facebook, follow the link below:
http://www.facebook.com/p.php?i=1646147841&k=AQAVgAJy52mb1-PB2xQ61qhtO-fF4-23pEw0pLALyeJvw_fAgUtdIEMjZXJKwFERNxWSvA&r

Already have an account? Add this email address to your account:
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=======================================
This message was sent to bioperl-l <at> bioperl.org. If you don't want to receive these emails from Facebook in
the future, please follow the link below to unsubscribe.
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 Facebook, Inc. Attention: Department 415 P.O Box 10005 Palo Alto CA 94303
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Jonathan Warren | 2 Feb 10:46
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Only 10 days left to register for DAS Workshop 2012

Only 10 days left to register for DAS Workshop 2012

DAS is currently being used to share annotations on genomes, protein
alignments, structural and interaction information.

If you are interested in sharing biological information the DAS workshop
below may be of interest to you.

Learn of and contribute to current developments in DAS such as: DAS in  
the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative  
annotation projects, DAS alternative formats.

Registration is open for the 2012 DAS workshop (27-29 February) at the
Genome Campus, Hinxton UK. If you are interested in attending, please
find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html 
  and
register via the web link at the bottom of the page. This workshop will
cater for novice to expert DAS users as each day is optional.

Please register early as places will be limited. Registration closes  
10 February 2012 - 12:00.

If you are interested in giving a 15 minute talk on the second day  
please email Jonathan Warren using jonathan.warren <at> sanger.ac.uk

Many thanks

The Sanger/EBI DAS team.

Jonathan Warren
(Continue reading)

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Puneet Kadimi | 2 Feb 04:16
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Check out my photos on Facebook

Hi Bioperl-l,

I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so
you can see it. First, you need to join Facebook! Once you join, you can also create your own profile.

Thanks,
Puneet

To sign up for Facebook, follow the link below:
http://www.facebook.com/p.php?i=1646147841&k=AQBEf7iEx7uHcyAqQibbKMtZbUnyPj4MjFuGd4aBfXw2itCG-JcHfP9uwAy7Du4m2r2eHw&r

Already have an account? Add this email address to your account:
http://www.facebook.com/n/?merge_accounts.php&e=bioperl-l%40bioperl.org&c=AQDNbz0MpsGYMKLlzfTt1q_SQWUXniSEkqIU1W3otHmU8Q

=======================================
This message was sent to bioperl-l <at> bioperl.org. If you don't want to receive these emails from Facebook in
the future, please follow the link below to unsubscribe.
http://www.facebook.com/o.php?k=24bbd2&u=1753461434&mid=593fd51G6883b2baG0G8
 Facebook, Inc. Attention: Department 415 P.O Box 10005 Palo Alto CA 94303
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Vivek Krishnakumar | 30 Jan 21:34
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`get_feature_by_name` not working after migrating to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend

Hello,

I have the following code snippet which is supposed to retrieve a certain 
gene "locus" feature from the backend database and use that to get the 
'start' and 'end' coordinate of the feature based on the 'strand' on which 
it is present.

my ($locus_obj, $gene_models) = get_annotation_db_features($locus, 
$gff_dbh);

sub get_annotation_db_features {
    my ($locus, $gff_dbh) = @_;

    my ($locus_obj) = $gff_dbh->get_feature_by_name('Gene' => '$locus');

    my ($end5, $end3) = $locus_obj->strand == 1
      ? ($locus_obj->start, $locus_obj->end)
      : ($locus_obj->end, $locus_obj->start);

    my $segment = $gff_dbh->segment($locus_obj->refseq, $end5, $end3);
    my @gene_models =
      $segment->features('processed_transcript:working_models', -attributes 
=> { 'Gene' => $locus });

    #will have to sort the gene models
    return ($locus_obj, \@gene_models);
}

Also, here is a snippet of the GFF3 file that is used to populate the 
backend database:
(Continue reading)

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Bradyjoel | 30 Jan 12:21
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Running into problems


HI all,

I'm quite new to bioperl and tried to write a script that creates a database
from a newly sequenced genome and then preforms a tblastn against a multiple
protein fasta file and then creates a blast report were only the results
that only preservers identity scores above 98%. However my script keeps
returning numerous errors and problems and since I have only a little
experience I cannot determine were I went wrong. I include the code that I
got so far in the attachment. Hope someone can help.
Regards Joel

http://old.nabble.com/file/p33228400/blast1.pl blast1.pl 
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Gmane