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Mgavi Brathwaite | 1 Dec 2010 20:13
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Problems loading BioPerl a

Hello,

I am receiving the following message on my MacOSX system after I run
"./Build install"

ERROR: Can't create '/usr/local/bin'
Do not have write permissions on '/usr/local/bin'

Any suggestions?

Mgavi
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Chris Fields | 1 Dec 2010 20:27
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Re: Problems loading BioPerl a

As the error msg indicates, your user account doesn't have write privs for /usr/local/bin'.  Suggestions
are one of the following:

1) Install it locally; see the instructions on the wiki for UNIX.  
2) Use 'sudo' to install it system-wide.  I don't recommend that unless needed if you are using bioperl-live
(or for any CPAN code for that matter).

chris

On Dec 1, 2010, at 1:13 PM, Mgavi Brathwaite wrote:

> Hello,
> 
> I am receiving the following message on my MacOSX system after I run
> "./Build install"
> 
> ERROR: Can't create '/usr/local/bin'
> Do not have write permissions on '/usr/local/bin'
> 
> Any suggestions?
> 
> Mgavi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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gvj | 2 Dec 2010 09:03
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how to get ID and parent from GFF


Hi,
This is something simple but I m nt able to figure it out whats going wrong.
I have a gff like this:
2       test    gene    2876    3540    0.38    +       .       ID=g1
2       test    transcript      2876    3540    0.38    +       .      
ID=g1.t1;Parent=g1
2       test    transcription_start_site        2876    2876    .       +      
.       Parent=g1.t1
2       test    exon    2876    3118    .       +       .       Parent=g1.t1
2       test    start_codon     3004    3006    .       +       0      
Parent=g1.t1
2       test    intron  3119    3225    1       +       .       Parent=g1.t1
2       test    CDS     3004    3118    1       +       0      
ID=g1.t1.cds;Parent=g1.t1
2       test    CDS     3226    3329    1       +       2      
ID=g1.t1.cds;Parent=g1.t1
2       test    exon    3226    3540    .       +       .       Parent=g1.t1
2       test    stop_codon      3327    3329    .       +       0      
Parent=g1.t1
2       test    transcription_end_site  3540    3540    .       +       .      
Parent=g1.t1

but when I am tring to get the ID value as follow:

my $gff = Bio::DB::GFF->new( -adaptor => "memory",
                             -gff    => $ARGV[0]);

for my $gff_gene ($gff->features("transcript")) {
print " YES the parent is there "  if( $gff_gene->has_tag('Parent') ) ;  #
(Continue reading)

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Chris Fields | 2 Dec 2010 15:53
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Re: how to get ID and parent from GFF

I'm not sure how this is done via Bio::DB::GFF, but try using Bio::DB::SeqFeature instead (which has
parent-child ties).  I think you need the tag value 'parent_id', but 'Parent' might work as well, with the
caveat I haven't tried this myself yet.

chris

On Dec 2, 2010, at 2:03 AM, gvj wrote:

> 
> Hi,
> This is something simple but I m nt able to figure it out whats going wrong.
> I have a gff like this:
> 2       test    gene    2876    3540    0.38    +       .       ID=g1
> 2       test    transcript      2876    3540    0.38    +       .      
> ID=g1.t1;Parent=g1
> 2       test    transcription_start_site        2876    2876    .       +      
> .       Parent=g1.t1
> 2       test    exon    2876    3118    .       +       .       Parent=g1.t1
> 2       test    start_codon     3004    3006    .       +       0      
> Parent=g1.t1
> 2       test    intron  3119    3225    1       +       .       Parent=g1.t1
> 2       test    CDS     3004    3118    1       +       0      
> ID=g1.t1.cds;Parent=g1.t1
> 2       test    CDS     3226    3329    1       +       2      
> ID=g1.t1.cds;Parent=g1.t1
> 2       test    exon    3226    3540    .       +       .       Parent=g1.t1
> 2       test    stop_codon      3327    3329    .       +       0      
> Parent=g1.t1
> 2       test    transcription_end_site  3540    3540    .       +       .      
> Parent=g1.t1
(Continue reading)

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Dave Clements | 4 Dec 2010 01:56
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2011 GMOD Spring Training, March 8-12

Applications are now being accepted for the 2011 GMOD Spring Training
course, a five-day hands-on school aimed at teaching new GMOD
administrators how to install, configure and integrate popular GMOD
components. The course will be held March 8-12 at the US National
Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as
part of GMOD Americas 2011.

Links:
   * http://gmod.org/wiki/2011_GMOD_Spring_Training
   * http://gmod.org/wiki/GMOD_Americas_2011
   * http://www.nescent.org/

These components will be covered:
   * Apollo - genome annotation editor
   * Chado - biological database schema
   * Galaxy - workflow system
   * GBrowse - genome viewer
   * GBrowse_syn - synteny viewer
   * GFF3 - genome annotation file format and tools
   * InterMine - biological data mining system
   * JBrowse - next generation genome browser
   * MAKER - genome annotation pipeline
   * Tripal - web front end to Chado databases

The deadline for applying is the end of Friday, January 7, 2011.
Admission is competitive and is based on the strength of the
application, especially the statement of interest. The 2010 school had
over 60 applicants for the 25 slots. Any application received after
deadline will be automatically placed on the waiting list.
(Continue reading)

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kris richardson | 6 Dec 2010 18:16
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eutils help

Dear Bioperl Users,

I am interested in generating the flanking sequences (20 nt from each side) from a list of ~500,000 SNPs,
from the dbSNP build 132.    

I tried using the perl API variation toolset to extract this information, however the script throws an
error when it encounters many of the recently discovered SNPs (from the 1000genomes data), as this tool is
still using the dbSNP 131 data.   

I read the bipoerl eUtils tool  might be used to obtain this info, but I can not find any example code in which
the dbSNP data is queried...   Does any one have any pointers or examples on how one might use efetch and
eUtils  to obtain the flanking sequence for a list of SNP rs #s?  

Thanks!

Kris
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Smithies, Russell | 6 Dec 2010 20:48
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Re: eutils help

I do this quite frequently and it's usually easiest to download the flanking fasta for the SNPs with their
batch query tool http://www.ncbi.nlm.nih.gov/SNP/batchquery.html then trim the sequences as
required with BioPerl.
I think you'll run into problems downloading that many SNPs reliably with eUtils and it's best to break it up
into smaller chunks.

--Russell

> -----Original Message-----
> From: bioperl-l-bounces <at> lists.open-bio.org [mailto:bioperl-l-
> bounces <at> lists.open-bio.org] On Behalf Of kris richardson
> Sent: Tuesday, 7 December 2010 6:17 a.m.
> To: bioperl-l <at> lists.open-bio.org
> Subject: [Bioperl-l] eutils help
> 
> Dear Bioperl Users,
> 
> I am interested in generating the flanking sequences (20 nt from each
> side) from a list of ~500,000 SNPs, from the dbSNP build 132.
> 
> I tried using the perl API variation toolset to extract this
> information, however the script throws an error when it encounters many
> of the recently discovered SNPs (from the 1000genomes data), as this
> tool is still using the dbSNP 131 data.
> 
> I read the bipoerl eUtils tool  might be used to obtain this info, but
> I can not find any example code in which the dbSNP data is queried...
> Does any one have any pointers or examples on how one might use efetch
> and eUtils  to obtain the flanking sequence for a list of SNP rs #s?
>
(Continue reading)

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C.J. | 7 Dec 2010 06:29
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extract protein sequence

Dear all,

I have download many polyprotein sequences from Genbank.
As the polyprotein sequence contains several mature peptides.
I want to extract my target mature peptide from these sequences.
Anyone would be kind to tell me any model in Bioperl can do this?
Thanks.

--

-- 
Regards!
C.J.
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Chris Fields | 7 Dec 2010 14:04
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Re: extract protein sequence

On Dec 6, 2010, at 11:29 PM, C.J. wrote:

> Dear all,
> 
> I have download many polyprotein sequences from Genbank.
> As the polyprotein sequence contains several mature peptides.
> I want to extract my target mature peptide from these sequences.
> Anyone would be kind to tell me any model in Bioperl can do this?
> Thanks.
> 
> -- 
> Regards!
> C.J.

You'll need to provide some example accessions to look at.  My guess is, if the mature peptide is described as
a feature, then yes.

chris
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Chris Fields | 7 Dec 2010 18:44
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Re: eutils help

The 'brief' return type format for dbSNP gives something like this (see below).  XML output (changing
'retmode' to XML instead of text) give much more information.

use strict;
use warnings;
use Bio::DB::EUtilities;

my $term = shift;
my $eutil  = Bio::DB::EUtilities->new(-eutil    => 'esearch',
                                      -db       => 'snp',
                                      -email    => 'foo <at> bar.org',
                                      -term     => $term,
                                      -usehistory => 'y',
                                      -retmax   => 100);

my $hist = $eutil->next_History || die "No history returned";

$eutil->set_parameters(-eutil   => 'efetch',
                       -history => $hist,
                       -retmode => 'text',
                       -rettype => 'brief');

print $eutil->get_Response->content."\n";

chris

On Dec 6, 2010, at 11:16 AM, kris richardson wrote:

> Dear Bioperl Users,
>
(Continue reading)

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Gmane