Francisco J. Ossandón | 22 Aug 17:50 2014
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Re: Proposal for bioperl-run

I have also looked 

I don't mind the moving of those modules but I would like to ask something. Any future updates to the moved
modules should also be added, if possible, to the modules that will remain v1.6.x branch? Or their
development would be freezed?? Or should they also be removed from there too??

I've been keeping the synchronicity of updated modules that were moved out of -live into their own repo with
their versions in v1.6.x branch (like Root and Coordinate), but the synch of WrapperBase when mixed into
other existing repo like Run will depend on if it start to depend on code of other Run modules or not.

On a side note, I just realized that there is an empty "hmmer3.pm" file in
"bioperl-live/Bio/Tools/Run"... It seems to have been added already empty in
https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e,
maybe by mistake. It appears to be the only empty file in the repo. Should I delete it??

Cheers,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces+fossandonc=hotmail.com <at> mailman.open-bio.org
[mailto:bioperl-l-bounces+fossandonc=hotmail.com <at> mailman.open-bio.org] En nombre de Mark A. Jensen
Enviado el: viernes, 22 de agosto de 2014 8:09
Para: Fields, Christopher J
CC: George Hartzell; bioperl-l <at> mailman.open-bio.org
Asunto: Re: [Bioperl-l] Proposal for bioperl-run

Thanks Chris-- yes, you must be right. I just did a quick grep for "StandAloneBlast" in the modules. I will
verify and leave bl2seq alone.
Will do everything in branches and then give the signal- cheers MAJ On 2014-08-21 23:50, Fields,
(Continue reading)

Mark A. Jensen | 22 Aug 03:49 2014
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Proposal for bioperl-run

All,
I'm starting to look at cleaning up bioperl-run so that, e.g., tests 
don't bork without a reasonable error message, are skipped 
appropriately, etc. As I do this, I'm finding that to fix certain 
issues, I need to consider mods to Bio::Tools::Run::WrapperBase and 
friends. Alas, these are in the bioperl-live distro!

Now, grepping for 'WrapperBase' in bioperl-live modules reveals only 
two that mention it:

Bio/Tools/Run/WrapperBase/CommandExts.pm
Bio/Tools/Run/StandAloneBlast.pm
Bio/Tools/Run/WrapperBase.pm

My simple proposal is to move these three modules from bioperl-live to 
bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, btw).

Thoughts?
MAJ
Cacau Centurion | 12 Aug 21:10 2014
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Extract sequences of CDS regions from Genbank formatted file

Hi all,

I was wondering if there is a way to directly extract all sequences of CDS regions from a Genbank formatted file using bioperl?

Yours,
Cacau
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RB | 11 Aug 15:31 2014
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www.ncbi.nlm.nih.gov:80 (Bad hostname)

Hello!

I'm trying to connect to a NCBI page and retrieve some information.
Basically I want to retrieve what is under "Representative" in 
http://www.ncbi.nlm.nih.gov/genome/?term=Xylella_fastidiosa
<http://www.ncbi.nlm.nih.gov/genome/?term=Xylella_fastidiosa>  . For this
I'm trying to use LWP::Simple or LWP::UserAgent, but in no way am I able to
retrieve the HTML.

Here is my code:
-------------------------------------------------------
#!/usr/local/bin/perl
use strict;
use warnings;
use autodie;
use Data::Dump;
use LWP::Simple qw(get);

my
$content=get('http://www.ncbi.nlm.nih.gov/genome/?term=Xylella_fastidiosa');

dd $content;
-------------------------------------------------------

But I get an undef from this code. I read through  this
post
<http://bioperl.996286.n3.nabble.com/Bio-Tools-Run-RemoteBlast-error-500-Can-t-connect-to-www-ncbi-nlm-nih-gov-80-td10210.html>

and here is the result of two different pings:
-------------------------------------------------------
Pinging www.wip.ncbi.nlm.nih.gov [130.14.29.110] with 32 bytes of data:
Request timed out.
Request timed out.
Request timed out.
Request timed out.

Ping statistics for 130.14.29.110:
    Packets: Sent = 4, Received = 0, Lost = 4 (100% loss),

-------------------------------------------------------
Pinging www.google.com [173.194.112.240] with 32 bytes of data:
Reply from 173.194.112.240: bytes=32 time=46ms TTL=53
Reply from 173.194.112.240: bytes=32 time=46ms TTL=52
Reply from 173.194.112.240: bytes=32 time=45ms TTL=53
Reply from 173.194.112.240: bytes=32 time=45ms TTL=53

Ping statistics for 173.194.112.240:
    Packets: Sent = 4, Received = 4, Lost = 0 (0% loss),
Approximate round trip times in milli-seconds:
    Minimum = 45ms, Maximum = 46ms, Average = 45ms
-------------------------------------------------------

So I guess this means there is something wrong on my side? What am I doing
wrong? Thanks for all the help

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Antony03 | 8 Aug 02:47 2014
Picon

fasta36 bug report

Hello,

There is a problem when I try to parse a fasta36 report. I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unrecognized alignment line (3) '>--'
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::SearchIO::fasta::next_result
/usr/share/perl5/Bio/SearchIO/fasta.pm:1148
STACK: ./Auto_Annot.pl:123
-----------------------------------------------------------

There is a '>--' after each alignment in fasta36 but not in fasta35. 

Consequently, I tried to parse a fasta35 alignment. There is no problem with
bioperl. However, the result is clearly not the same between both (fasta35
and fasta36).

fasta35 gives only 1 alignment: http://pastebin.com/f4NdYJCt

while fasta36 gives 3 alignments: http://pastebin.com/ADeKJ4GC

What I'm doing wrong with fasta35? It is probably not normal that it misses
almost 2 perfect alignments on 3.

Thanks you!

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Fields, Christopher J | 4 Aug 23:05 2014

Re: help!

All,

The master branch on github is undergoing significant changes that will break your code; in short, it is missing several modules that were removed due to our work on modularization.  If you really need to grab the latest stable code, I recommend either getting the latest CPAN release (v1.6.924, just released a month ago) or using the ‘v1.6.x’ branch on GitHub, which we have been routinely patching with fixes to the main branch.

If needed we can switch the default checkout branch to ‘v1.6.x' to make things easier (so far there has been no consensus about this, so I am leaving it as is for the time being).

chris

On Aug 1, 2014, at 1:20 PM, Tess Cherlin <tess.cherlin <at> gmail.com> wrote:

Hi Dave, Chris, Cassandra and others,

I was following the wonderful directions that Dave wrote and have made it to an almost similar end as Cassandra.


ncfa-2-3502-ap3:~ Vi$ perl -e "use Bio::SeqIO;"
Base class package "Bio::Root::Root" is empty.
    (Perhaps you need to 'use' the module which defines that package first.)
 at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.
Compilation failed in require at (eval 1) line 3.
    ...propagated at /System/Library/Perl/5.8.8/base.pm line 85.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Simple.pm line 87.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.
Compilation failed in require at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
ncfa-2-3502-ap3:~ Vi$ 


I see that there are many items that were not compiled "aborted", is that something I need to do separately? I'm sorry but I got lost when Dave and Chris began discussing the stuff at the bottom of this chain. So if someone could explain a solution simply I would greatly appreciate it!

Thank you!

Tess

On Tuesday, February 7, 2012 3:38:12 PM UTC-6, Dave Messina wrote:
I will take the opportunity to shamelessly pimp my no-install install
instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
Casandra is just looking to get started with BioPerl, messing with external
libs and configs is probably overkill.

Best,
Dave


 There’s a quickie, “zero-install” way to get BioPerl on your system.

    1) Okay, click here to download bioperl as a zip file:

    https://github.com/bioperl/bioperl-live/zipball/master


    when it's done downloading, unzip it if your computer hasn’t done it
automatically. On the
    command line, you would do:

         unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip

    or whatever the file is called. You should then have a folder with some
ugly name like

    bioperl-bioperl-live-558467a

    3) rename that to

    bioperl-live

    4) move that folder to wherever you want to keep it. I keep mine in a
directory called src in my
        home directory.

    So on my computer if I go to the command line and cd to that folder and
type pwd I get:

    /Users/dave/src/bioperl-live

    5) in the terminal, cd to your home directory.

    6) see if you have a file named .bash_profile by typing

    ls -l ~/.bash_profile

    7) if so, open that file in your favorite editor. if the file doesn't
exist, just create the file.

    8) put this line in your .bash_profile

             export PERL5LIB=/Users/dave/src/bioperl-live

    (obviously replacing my path info with wherever you chose to put
bioperl)

    9) save and close your .bash_profile

  10) open a new terminal window so that the change will take effect.

  11) on the command line of the new terminal, type

               perl -e "use Bio::SeqIO;"

    If that works, then you have "installed" bioperl. Yay!







On Tue, Feb 7, 2012 at 22:12, Scott Cain <sc... <at> scottcain.net> wrote:

> Yes, but those doc don't address exactly the problem Cassandra is
> having, that she wants to use local::lib, but there need to be some
> prereqs installed, but they can't be because she chose to use
> local::lib, and it's not installed.  That's all fine if you're not a
> newbie and know how to properly install the prereqs before using the
> cpan shell, but when following instructions that say "use local::lib",
> I find that the instructions are completely insufficient in actually
> getting the desired software installed.  Thus the need for a good
> tutorial.
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfi... <at> illinois.edu>
> wrote:
> > I guess one key question is where these CPAN installation instructions
> come
> > from.  They're a bit odd, and if this is from the wiki we need to do some
> > updating.
> >
> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> > single perl version.
> >
> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
> >
> > In my case I use perlbrew (which is all local by default, and allows
> > switching between perl versions).  Highly recommend using either simple
> > local::lib or perlbrew in combination with cpanm.
> >
> > https://metacpan.org/module/perlbrew
> > https://metacpan.org/module/cpanm
> >
> > chris
> >
> >
> >
> > On 02/07/2012 02:55 PM, Scott Cain wrote:
> >>
> >> hi Cassandra,
> >>
> >> I don't have an answer for you at the moment.  It seems to me that
> >> using local::lib is a good idea, but I've never found a good tutorial
> >> for using it, so I haven't.  Perhaps someone else on the list can
> >> suggest one.
> >>
> >> The other thing I just wanted to mention as the admin that approved
> >> your message--I came very close to deleting it from the queue without
> >> looking at it because it is not unusual for spam messages to have
> >> generic subjects like "help!"  (just for future reference :-)
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasa... <at> gmail.com>  wrote:
> >>>
> >>> 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:
> >>>
> >>>  >cpan
> >>>  cpan>install Module::Build
> >>>  cpan>o conf prefer_installer MB
> >>>  cpan>o conf commit
> >>>  cpan>q
> >>>
> >>>      * Install the expat library by whatever method is
> >>>        appropriate for your system.
> >>>
> >>>      * If your expat library is installed in a non-standard location,
> >>>        tell CPAN about it:
> >>>
> >>>  >cpan
> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> >>> EXPATINCPATH=/non-standard/include"
> >>>  cpan>o conf commit
> >>>
> >>> --------------
> >>>
> >>> And I think I did "Upgrade CPAN properly" but when I tried the next one
> >>> it
> >>> started asking too many things to me, and finally it stopped due to
> "some
> >>> problems". In text file you can see the whole process.
> >>> What did I do wrong?
> >>>
> >>>
> >>> After solving these preliminary steps, what should I do? What exactly
> >>> .tar
> >>> or .whatever should I download to install?
> >>>
> >>> I don't see the difference between installing it through "built.PL" or
> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
> >>> MAC.
> >>>
> >>> * I went to Fink webpage and what I expected to see was "hello!
> download
> >>> Bioperl simply clicking here!" but far from this, what it seems is that
> >>> first I have to download some kinf of Fink-program before starting with
> >>> Bioperl... is it something close to this?
> >>>
> >>> I'm sorry, too many questions... But I really want to learn to use
> >>> Bioperl
> >>> but I have no people to ask it face to face.
> >>>
> >>> Thank you so much,
> >>>
> >>> Casandra
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Biop... <at> lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Biop... <at> lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> _______________________________________________
> Bioperl-l mailing list
> Biop... <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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Ashton Trey Belew | 31 Jul 05:25 2014
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Bio::SearchIO::infernal.pm


  Good evening,
  I was fiddling with cmsearch this evening and discovered that the
current infernal parser does not play well with the new version (1.1)
of infernal.  I am currently hacking on the function parse_latest() in
an attempt to handle the differences in formats but have hit a bit of
a wall in picking up the accessions and descriptions from the cmsearch
output.
  In a peculiar turn of events, if parse_latest does not find the
accession/description fields, it seems to repeat the PARSER: loop
indefinitely, in my case repeating $self->_readline on the the 10th hit.

  I will keep poking at it this evening, but if anyone has made
greater headway, I would love some pointers.

  Thank you for your time,
 -Trey
Francesco Strozzi | 30 Jul 10:46 2014
Picon

EU OBF Codefest - September 18th and 19th 2014 <at> EBI - Hinxton UK

Dear all,
apologies if you receive this multiple times.

We are glad to announce that we are organising the European edition of
the OBF Codefest, which will take place on September 18th and 19th at
the EBI in Hinxton, UK. This is the second OBF Codefest this year, the
first was held this month in Boston just before the BOSC and ISMB
conferences and in September we will have the chance to expand and
carry on the work and discussions started in July in the USA.

The EU Codefest will precede the Genome
Informatics Conference in Cambridge, so we hope that developers
attending the main conference will be also interested in joining us
for a couple of days of coding and discussions on collaborative
projects and new ideas. The main topics that were proposed so far are:

* The OpenBio projects development (BioPerl, BioPython, BioRuby, BioJava)
* Semantic web technologies for biological data (e.g. RDF, OWL)
* Software deployment and bioinformatics pipelines, including
CloudBiolinux, Docker and GNU GUIX
* NoSQL databases and NGS data mining
* Biological data visualisation with e.g. D3/JS and BioJS.

We of course invite attendees to add other topics of interest.

For more information, you can visit the OBF Wiki page, which includes
also information on accommodation and registration:
http://www.open-bio.org/wiki/EU-Codefest_2014
If you plan to attend, please use the link in the registration section
and complete the simple steps on the EBI website, so that
we can be aware of the total number of attendees and arrange the
organisation accordingly. Registration is also completely free.

We will be grateful if you could also share this announce over your
network and social media, this will help spreading the word.

Thanks and we hope to see many of you in September!

Francesco Strozzi
James Malone
Raoul Bonnal
Pjotr Prins
Francisco J. Ossandón | 25 Jul 21:00 2014
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"->bits" behaviour in HMMer parsing

Hello everyone,

I was checking Bio::SearchIO and found that there is an inconsistency regarding Bits value for $hit and $hsp when parsing HMMer outputs.

 

HMMer results don’t use Bits, so when Bits are requested from $hit, it returns 0 from the HMMERHit module (“sub bits { return 0 }”), but when Bits are requested from $hps, it goes to the SimilarityPair and Similarity modules and they return ‘undef’. Since $hit->bits already return 0, I think it would be consistent to also return 0 from $hsp->bits… Adding “sub bits { return 0 }” to the HMMERHSP module would do the trick.

 

What do you think?? Is it ok for me to add this to HMMERHSP and make it consistent or there could be something wrong with it??

 

Cheers,

 

Francisco

 

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Fields, Christopher J | 24 Jul 20:14 2014

Re: length of hit->description

That is unusual.  The only recourse is to submit a bug report to Github and attach an example report giving the
error.  My feeling is that this might be a change in the output for FASTA.

chris

On Jul 24, 2014, at 12:54 PM, Antony Vincent <antony.vincent.1 <at> ulaval.ca> wrote:

> Hello,
> 
> Thank you for the quick answer.
> 
> Here is a part of the code:
> #fasta parameters
> my $fh;  
> my $query = 'MyORF.tfa';
> my $library = "$library";                 
> my $fasta   = 'fasta35'; 
> 
> 
> # The fasta parsing part
> my $command = "$fasta -b 1 $query $library";
> 
> open $fh,"$command |" || die("cannot run fasta cmd of $command: $!\n");
> 
> my $searchio  = Bio::SearchIO->new(-format => 'fasta', -fh => $fh);
> while( my $result = $searchio->next_result ) {
>  ## $result is a Bio::Search::Result::ResultI compliant object
>  while( my $hit = $result->next_hit ) {
>    ## $hit is a Bio::Search::Hit::HitI compliant object
>    while( my $hsp = $hit->next_hsp ) {
>      ## $hsp is a Bio::Search::HSP::HSPI compliant object
>      if( $hsp->length('total') > $length*0.85) {
>        if ( $hsp->frac_conserved >= 0.65) {
> 
> 	
> 	print $hit->description(500), "\n";
> 	
> 
> 
> 				}
>            }
> 		}
> 	}  
> }
> 
> The correct result should be :
> repB	putative plasmid replication protein RepB
> 
> And I get:
> repB	putative plasmid replication protein R
> 
> Thank you,
> 
> Antony
> 
> Le 2014-07-24 à 13:48, Fields, Christopher J <cjfields <at> illinois.edu> a écrit :
> 
>> You’ll have to be more explicit.  What is the analysis (BLAST, FASTA, BLAT, etc)?  What is the expected
result?  
>> 
>> Most of the above parsers will take the hit name as the first set of non-whitespace characters, and
anything after that is put into the description.
>> 
>> chris
>> 
>> On Jul 24, 2014, at 12:04 PM, Antony03 <antony.vincent.1 <at> ulaval.ca> wrote:
>> 
>>> Hello,
>>> 
>>> When I use hit->description I get a truncated result like this:
>>> 
>>> repB putative plasmid replication protein R
>>> 
>>> I tried hit->description(500) and I get the same result.
>>> 
>>> Is there something wrong?
>>> 
>>> Thanks
>>> 
>>> 
>>> 
>>> --
>>> View this message in context: http://bioperl.996286.n3.nabble.com/length-of-hit-description-tp17596.html
>>> Sent from the Bioperl-L mailing list archive at Nabble.com.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l <at> mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
Antony03 | 24 Jul 19:04 2014
Picon

length of hit->description

Hello,

When I use hit->description I get a truncated result like this:

repB putative plasmid replication protein R

I tried hit->description(500) and I get the same result.

Is there something wrong?

Thanks

--
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Gmane