headers
jdeuts01 | 1 Dec 2011 15:09

question


Dear Bioperl,
       This is my first experience with bioperl and I need help please.
1. The version of bioperl is 1.6.1 and have also installed Bundle-BioPerl 2.1.8 and mGen 1.03.    I was unable
to install Bribes and trouchelle DB.     Will this prevent the BioPerl package from functioning correctly?
2. The operating platform is windows 7 - 64 bit using ActiveState - Perl v5.12.2
3. The script is as follows:
#!/usr/bin/perl
# Write a script using OOP to write protein sequences to the file fasta.txt.use strict;use warnings;use Bio::SeqIO::fasta;
# Declare and initialize input and output files.my $protein_fasta = "protein.fa";my $protein_out = ">fasta.txt";
# Setup objects for input and output.my $seq_in = Bio::SeqIO->new(-file => "$protein_fasta", -format =>
'Fasta');my $seq_out = Bio::SeqIO->new(-file => "$protein_out", -format => 'fasta');
# Establish while loop using "next_seq" method # to read in multiple sequences from "protein.fa" file# one
by one until none were remaining.while(my $seq = $seq_in -> next_seq){		$seq_out->write_seq($seq);}
The information is successfully written to the file: fasta.txt. 
4. Receiving the following error messages: 
Replacement list is longer than search list at C:/Perl64/site/lib/Bio/Range.pm line 251.Subroutine
_initialize redefined at C:/Perl64/site/lib/Bio\SeqIO\fasta.pm line 92.Subroutine next_seq
redefined at C:/Perl64/site/lib/Bio\SeqIO\fasta.pm line 112.Subroutine write_seq redefined at
C:/Perl64/site/lib/Bio\SeqIO\fasta.pm line 193.Subroutine width redefined at
C:/Perl64/site/lib/Bio\SeqIO\fasta.pm line 272.Subroutine preferred_id_type redefined at
C:/Perl64/site/lib/Bio\SeqIO\fasta.pm line 295.
Thanks in advance for your help.John Deutsch
Permalink | Reply | 0 comments |
headers
Boddu, Jayanand | 1 Dec 2011 17:38
Favicon

Chromosome coordinates

Hello
I am newbie to Perl scripts.
I have a file with short reads mapped to the MAIZE genome
The format is a simple BLASTN output.
READ_ID

Chr

% Similarity

Alignment

Mismatches

Gaps

READ Start

READ End

Chr Start

Chr End

E Value

Score

READ1
(Continue reading)

Permalink | Reply | 4 comments |
headers
Scott Cain | 1 Dec 2011 17:59
Favicon

Re: Chromosome coordinates

Hi Jay,

Since the maize GFF file is likely to be fairly large, I would consider
putting it in a database, using either Bio::DB::GFF if it is GFF2 or
Bio::DB::SeqFeature::Store if it is gff3.  Then you can use the methods
that come along with either of those modules to search regions for for
genes.  They both support a get_features_by_location method, so you could
get the range for each of the regions you want to look at, and check the
database with that method to see if anything is there.

Scott

On Thu, Dec 1, 2011 at 11:38 AM, Boddu, Jayanand <jboddu <at> illinois.edu>wrote:

> Hello
> I am newbie to Perl scripts.
> I have a file with short reads mapped to the MAIZE genome
> The format is a simple BLASTN output.
> READ_ID
>
> Chr
>
> % Similarity
>
> Alignment
>
> Mismatches
>
> Gaps
>
(Continue reading)

Permalink | Reply | 3 comments |
headers
Jason Stajich | 1 Dec 2011 18:31
Picon
Gravatar

Re: Chromosome coordinates

You might try using BEDtools, intersectBED which can do a lot of what you are doing in simple command line program.

Jason
On Dec 1, 2011, at 8:59 AM, Scott Cain wrote:

> Hi Jay,
> 
> Since the maize GFF file is likely to be fairly large, I would consider
> putting it in a database, using either Bio::DB::GFF if it is GFF2 or
> Bio::DB::SeqFeature::Store if it is gff3.  Then you can use the methods
> that come along with either of those modules to search regions for for
> genes.  They both support a get_features_by_location method, so you could
> get the range for each of the regions you want to look at, and check the
> database with that method to see if anything is there.
> 
> Scott
> 
> 
> On Thu, Dec 1, 2011 at 11:38 AM, Boddu, Jayanand <jboddu <at> illinois.edu>wrote:
> 
>> Hello
>> I am newbie to Perl scripts.
>> I have a file with short reads mapped to the MAIZE genome
>> The format is a simple BLASTN output.
>> READ_ID
>> 
>> Chr
>> 
>> % Similarity
>>
(Continue reading)

Permalink | Reply | 0 comments |
headers
Juan Jovel | 1 Dec 2011 18:36
Picon
Favicon

Error when using SearchIO


Hello Everybody!
I have been running endless standalone Blasts these days, in two different clusters. The first one runs on
Rock Linux, while the other one on Devian. In the Rock Linux one, when I use SeachIO to parse my blastp or
blastx reports, I get invariably a message:
"Replacement list is longer than search list at
/share/apps/lib/perl5/site_perl/5.14.1/Bio/Range.pm line 251"
What it does mean? Would it have any effect on my parsing results?
Thanks, 
JUAN
Permalink | Reply | 1 comment |
headers
Fields, Christopher J | 1 Dec 2011 20:03
Favicon
Gravatar

Re: Error when using SearchIO

On Dec 1, 2011, at 11:36 AM, Juan Jovel wrote:

> Hello Everybody!
> I have been running endless standalone Blasts these days, in two different clusters. The first one runs on
Rock Linux, while the other one on Devian. In the Rock Linux one, when I use SeachIO to parse my blastp or
blastx reports, I get invariably a message:
> "Replacement list is longer than search list at
/share/apps/lib/perl5/site_perl/5.14.1/Bio/Range.pm line 251"
> What it does mean? Would it have any effect on my parsing results?
> Thanks, 
> JUAN

This is a bug that was fixed, I think this was in the latest BioPerl release (1.6.901).  There was a
transliteration error that produced this warning, but otherwise it's harmless. The warning is perl
version dependent, I think it pops up in perl 5.12 and up.  This user post (about halfway down) runs into the
same issue: http://www.sysarchitects.com/bioperl.

chris
Permalink | Reply | 0 comments |
headers
Dave Messina | 1 Dec 2011 23:02
Picon
Picon
Favicon

Re: re trieving blast multiple alignment in fasta form

Hi Eric,

Wait, do you want multiple pairwise alignments in your output FASTA file,
or a single multiple alignment of your query and all the hits?

If the former, get_aln() will give you one pairwise alignment per hsp, but
you'll need to move the output file creation statement (my $alnIO = ...)
before the loops so it gets created only once. Then, when you do the write
statement ($alnIO->write_aln($aln);), all of the alignments will go to the
same file.

If on the other hand you'd like to have a multiple alignment between a
query and all of its hits, you'll have to take the IDs of the hits, pull
the corresponding sequences out of the database, and then run a multiple
alignment algorithm on them.

Dave
Permalink | Reply | 0 comments |
headers
Claudio Scuoppo | 2 Dec 2011 23:50
Picon

List of genes from genomic intervals

Hi,

I am new to BioPerl. I was wondering what`s the best strategy to get
the genes contained in a a series of human genomic interval.
Basically, I have a table with:

Chromosome Start End

Which module should I be looking at?
Thanks,
Claudio
Permalink | Reply | 0 comments |
headers
Adam Witney | 5 Dec 2011 12:09
Picon
Favicon

Bio::Graphics imagemap and padding

Hi,

Image maps seem to be out of position if you use padding in the Panel, like this:

my $panel = Bio::Graphics::Panel->new( ….. -pad_left  => 20, -pad_right => 20 …… );

Without these options, the image map is fine. Is this a known issue?

Also on a side note, I noticed that when using Bio::Graphics with Dancer, some of the CGI code was blocking
somewhere (I found a reference to a similar problem with CGI and Catalyst), swapping CGI with
HTML::Entities fixes it:

sub create_web_map {
….
	eval "require HTML::Entities" unless HTML::Entities->can('encode_entities');
….
	my $title  = HTML::Entities::encode_entities($self->make_link($tr,$feature,1));
 	my $target = HTML::Entities::encode_entities($self->make_link($tgr,$feature,1));
…..
}

Thanks

Adam
Permalink | Reply | 0 comments |
headers
Amin Momin | 6 Dec 2011 00:00
Picon

SimpleAlign and consensus_string

Hi ,

I am generating a consensus sequence by aligning two protein homologs
using Bio::Tools::Run::Alignment::TCoffee. However, I am unable to
understand the criteria consensus_string() method of simpleAlign uses
to determine the consensus at position with dissimilar aminoacids/
nucleotide. Also how would the % cutoffs provided to
consensus_string() affect the outcome.

Thanks,
Amin
Permalink | Reply | 2 comments |

Gmane