Adam Sjøgren | 26 May 10:34 2015
X-Face

Temporary file names in Bio::Tools::Run::StandAlonwWUBlast

  Hi.

I just noticed a problem with the temporary file names that
Bio::Tools::Run::StandAloneWUBlast uses.

wublast automatically tries to ungzip files that have names that match
certain patterns - noticably files ending in "_Z".

B:T:R:StandAloneWUBlast uses B:T:R:StandAloneBlast::_setinput() to
generate a temporary file for the query sequence.

_setinput() calls File::Temp::tempfile() without a SUFFIX (or a
TEMPLATE), which means that when you are (un)lucky, the temporary file
name becomes something like /tmp/i0311ckB_Z - which wublastp then tries
to ungzip, which fails.

I have created a pull request to add TEMPLATE and SUFFIX to
B:T:R:StandAloneBlast::_setinput()'s calls to tempfile():

 * https://github.com/bioperl/bioperl-run/pull/15

  Best regards,

    Adam

--

-- 
                                                          Adam Sjøgren
                                                    adsj <at> novozymes.com

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Peter Cock | 5 May 15:42 2015

Fwd: [blast-announce] New Version of BLAST XML output

FYI - time to update all the Bio* parsers with the new BLAST XML variant...

Peter

---------- Forwarded message ----------
From: Mcginnis, Scott (NIH/NLM/NCBI) [E] <mcginnis <at> ncbi.nlm.nih.gov>
Date: Tue, May 5, 2015 at 2:32 PM
Subject: [blast-announce] New Version of BLAST XML output
To: NLM/NCBI List blast-announce <blast-announce <at> ncbi.nlm.nih.gov>

The NCBI is now making a new version of the BLAST XML available for
testing.  Read about the changes and how to access BLAST results using
the new XML at ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf
wgallin | 1 May 00:10 2015
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WP_ Accession Protein records

I've been working on scripts that update a small database that I maintain from a selection or records in GENBANK.

I've encountered a problem and am wondering if anyone can suggest a work-around.

I am finding that the protein records that have been replaced by reference to a single entry in the WP_ series accessions in RefSeq have been annotated as removed, rather than replaced.

The result is that when I use a gi number from one of the original (pre-consolidation) entries to recover a record using Bio::DB::Eutilities tools to return a Document Summary I get a record that has the status listed as dead, rather than Replaced by WP_XXXXX.

In the on-line web interface, however, the search has a redirection to the appropriate WP_XXXXX record.

An example is gi number 71065499.

So my question is, is there a Feature other than status in the Document Summary record that gives forwarding information for records replaced by WP_XXXX series records?

Warren Gallin
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Warren Gallin | 27 Apr 19:35 2015
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Using Utilities to retrieve multiple coding sequences for identical (WP_) protein sequences

With the advent of the WP_   accession series in RefSeq there is no longer a direct link between a single
protein sequence and its encoding nucleotide sequence.

It is possible to find the multiple individual nucleotide records encoding the identical protein
sequences on the Web interface through the “Identical Proteins” link, which generates a list of all
of the coding sequences for the identical protein sequence.

Is there any way to work through these linkages using Bio::DB::Utilities?

Thanks,

Warren Gallin
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Warren Gallin | 20 Apr 22:33 2015
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inc::TestHelper

Further to my problem installing Bio::DB::Utilities.

Below is a chunk of the the output near the top of the material that plays out during attempted installation
using CPAN

Running make for C/CJ/CJFIELDS/Bio-EUtilities-1.73.tar.gz
---- Unsatisfied dependencies detected during ----
----    CJFIELDS/Bio-EUtilities-1.73.tar.gz   ----
    inc::TestHelper [build_requires]
Running install for module 'inc::TestHelper'

  The module inc::TestHelper isn't available on CPAN.

  Either the module has not yet been uploaded to CPAN, or it is
  temporary unavailable. Please contact the author to find out
  more about the status. Try 'i inc::TestHelper'.

inc::TestHelper is not listed as a module in CPAN

cpan[5]> i inc::TestHelper                                                                          
Module id = inc::TestHelper
    CPAN_VERSION undef
    CPAN_FILE    N/A
    INST_FILE    (not installed)

It is, however, a file that has been downloaded as part of the Utilities 1.7.3 CPAN download

/Users/wgallin1/.cpan/build/Bio-EUtilities-1.73-lE1tKP/inc/TestHelper.pm

So for some reason CPAN is not recognizing the presence of this module, and since it is listed as a dependency
it is failing the install.

Does anyone have a clue as to why this is happening?

Warren Gallin
黎新年 | 20 Apr 14:03 2015

Re: Bioperl-l Digest, Vol 144, Issue 6




------------------ Original ------------------
From:  "bioperl-l-request";<bioperl-l-request <at> mailman.open-bio.org>;
Date:  Mon, Apr 20, 2015 08:00 PM
To:  "bioperl-l"<bioperl-l <at> mailman.open-bio.org>;
Subject:  Bioperl-l Digest, Vol 144, Issue 6

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Today's Topics:

   1.  Problem Installing Bio::DB::EUtilities (Warren Gallin)


----------------------------------------------------------------------

Message: 1
Date: Sun, 19 Apr 2015 13:37:25 -0600
From: Warren Gallin <wgallin <at> ualberta.ca>
To: BioPerl List <Bioperl-l <at> mailman.open-bio.org>
Subject: [Bioperl-l] Problem Installing Bio::DB::EUtilities
Message-ID: <D0F7DD50-C606-4D8C-8706-8DAED1A27C98 <at> ualberta.ca>
Content-Type: text/plain; charset=utf-8

After a machine crash I have had to install all my software anew, using OS X 10.10.3 on a brand new macBook Pro.

I was able to install BioPerl, but when I have tried to install Bio::DB::EUtilities I consistently get the following failure after the tests are run:
??????????????????????????????????????????????????????????????????????????

[clipped]

All tests successful.
Files=21, Tests=756,  3 wallclock secs ( 0.13 usr  0.04 sys +  2.91 cusr  0.47 csys =  3.55 CPU)
Result: PASS
  CJFIELDS/Bio-EUtilities-1.73.tar.gz
Tests succeeded but one dependency not OK (inc::TestHelper)
  CJFIELDS/Bio-EUtilities-1.73.tar.gz
  [dependencies] -- NA
Failed during this command:
 CJFIELDS/Bio-EUtilities-1.73.tar.gz          : make_test NO one dependency not OK (inc::TestHelper)


???????????????????????????????????????????????????????????

inc::Test is not, as far as I can tell, a separate module, but rather something internal to Bio::DB::EUtilities

So my question is, how do I get Utilities installed so I can access NCBI data?

Warren Gallin




------------------------------

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End of Bioperl-l Digest, Vol 144, Issue 6
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Warren Gallin | 19 Apr 21:37 2015
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Problem Installing Bio::DB::EUtilities

After a machine crash I have had to install all my software anew, using OS X 10.10.3 on a brand new macBook Pro.

I was able to install BioPerl, but when I have tried to install Bio::DB::EUtilities I consistently get the
following failure after the tests are run:
——————————————————————————————————————————————————————————————————————————

[clipped]

All tests successful.
Files=21, Tests=756,  3 wallclock secs ( 0.13 usr  0.04 sys +  2.91 cusr  0.47 csys =  3.55 CPU)
Result: PASS
  CJFIELDS/Bio-EUtilities-1.73.tar.gz
Tests succeeded but one dependency not OK (inc::TestHelper)
  CJFIELDS/Bio-EUtilities-1.73.tar.gz
  [dependencies] -- NA
Failed during this command:
 CJFIELDS/Bio-EUtilities-1.73.tar.gz          : make_test NO one dependency not OK (inc::TestHelper)

———————————————————————————————————————————————————————————

inc::Test is not, as far as I can tell, a separate module, but rather something internal to Bio::DB::EUtilities

So my question is, how do I get Utilities installed so I can access NCBI data?

Warren Gallin

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Fields, Christopher J | 13 Apr 21:48 2015

Re: Problems installing on Mac OS 10.9.5

Seem you are installing to the system perl (see the ‘Permission denied’ issue).   You can install using ‘sudo’ but I highly suggest not installing this into your system Perl if possible, namely b/c it can cause problems down the road.  You should look into using homebrew to install a localized perl, then use that new version.  

Alternatively, you can use perlbrew (which I highky recommend as you can install multiple perl versions locally if needed):


chris

On Apr 13, 2015, at 2:16 PM, Mgavi Brathwaite <lsbrath <at> gmail.com> wrote:

Hi Chris,

I've done the install from CPAN and at the end of the install I'm informed that nothing installed.

Check attachment<Screen Shot 2015-04-13 at 3.15.01 PM.png>

On Sun, Apr 12, 2015 at 11:03 AM, Fields, Christopher J <cjfields <at> illinois.edu> wrote:
You’ll have to be more specific than that.  What specific problems did you encounter?  

chris

On Apr 12, 2015, at 12:21 AM, Mgavi Brathwaite <lsbrath <at> gmail.com> wrote:

Having difficulty installing BioPerl on my MacOS 10.9.5. Any suggestions?

Brath

-- 
Mgavi Elombe Brathwaite, MSc.
"Felix qui nihil debet"
"Happy is he who owes nothing"
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-- 
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"Felix qui nihil debet"
"Happy is he who owes nothing"

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Mgavi Brathwaite | 12 Apr 07:21 2015
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Problems installing on Mac OS 10.9.5

Having difficulty installing BioPerl on my MacOS 10.9.5. Any suggestions?

Brath

--
Mgavi Elombe Brathwaite, MSc.
"Felix qui nihil debet"
"Happy is he who owes nothing"
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Adam Sjøgren | 9 Apr 14:47 2015
X-Face

EMBL file with space before quoted, multi-line qualifier value

  Hi.

I just stumbled over an EMBL file that has space after equal-sign that
follows the qualifier name.

BioPerl doesn't parse folded lines when that happens, because the "-char
is expected to be the first character after the '='.

I have whittled it down to this example:

ID   TEST standard; DNA; 10 BP.
XX
AC   TEST;
XX
DT   09-APR-2015
XX
DE   Test of space before quoted qualifier.
XX
XX
FH   Key             Location/Qualifiers
FT   CDS             1..10
FT                   /*tag= x
FT                   /gene= "someT"
FT                   /product= "somewordandt extthatisquite lon
FT                   gandthereforewraps"
XX
SQ   Sequence 10 BP; 10 A; 0 C; 0 G; 9 T; 0 U; 0 Other;
     aaaaaaaaaa       10
//

And this "one"-liner:

  ~$ perl -e 'use warnings; use strict; use Bio::SeqIO; my
$in=Bio::SeqIO->new("-file"=>"white_space.embl", "-format"=>"embl"); my $seq=$in->next_seq;
foreach my $feature ($seq->all_SeqFeatures) { print $feature->primary_tag . "\n"; map { print "  /" . $_ .
"=" . (join " ", $feature->get_tag_values($_)) . "\n"; } $feature->get_all_tags }'

  ------------- EXCEPTION: Bio::Root::Exception -------------
  MSG: Can't see new qualifier in: gandthereforewraps"
  from:
  /*tag= x
  /gene= "someT"
  /product= "somewordandt extthatisquite lon
  gandthereforewraps"

  STACK: Error::throw
  STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
  STACK: Bio::SeqIO::embl::_read_FTHelper_EMBL /usr/share/perl5/Bio/SeqIO/embl.pm:1361
  STACK: Bio::SeqIO::embl::next_seq /usr/share/perl5/Bio/SeqIO/embl.pm:400
  STACK: -e:1
  -----------------------------------------------------------

shows the error.

If I add this patch:

--- Bio/SeqIO/embl.pm.orig	2015-04-09 14:27:08.035573910 +0200
+++ Bio/SeqIO/embl.pm	2015-04-09 14:27:46.952373300 +0200
 <at>  <at>  -1358,7 +1358,7  <at>  <at> 
     # intact to provide informative error messages.)
   QUAL: for (my $i = 0; $i <  <at> qual; $i++) {
         $_ = $qual[$i];
-        my( $qualifier, $value ) = m{^/([^=]+)(?:=(.+))?}
+        my( $qualifier, $value ) = m{^/([^=]+)*(?:=\s*(.+))?}
             or $self->throw("Can't see new qualifier in: $_\nfrom:\n"
                             . join('', map "$_\n",  <at> qual));
         if (defined $value) {

then the output is:

  CDS
    /*tag=x
    /gene=someT
    /product=somewordandt extthatisquite lon gandthereforewraps

which seems more reasonable, even if the format does not allow
whitespace after the =-sign (I haven't checked).

What do you think?

  Best regards,

    Adam

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                                                    adsj <at> novozymes.com

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Wilson, Colin (CC | 4 Mar 01:13 2015
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Bio:Seq->translate with orf=1; behavior change between 1.5 and 1.6

I've got an older application that I'm migrating from BioPerl 1.5 to 1.6.923, and it didn't pass testing due
to a change in the behavior of Bio:Seq::translate between 1.5 and 1.6

Per  the bioperl documentation Seq->translate(-orf=> 1) should return the first orf in a sequence.   It
appears to be returning the orf upstream of the first stop codon, so an internal out of frame orf is found
instead of a full length orf.

Here's my test code.   It passes in 1.5, fails in 1.6.  Is there a switch or different parameter to get the old
behavior?  Is this a bug or intentional change in translate?  
------------
use strict;
use Bio::Seq;

my ($bs, $prot, $orf0, $orf1, $orf) ;
$bs = Bio::Seq->new( -seq           => "ATGAATGTAAATAA",
		   -display_id       => "TestSequence",
		   -alphabet         => 'dna' );

$orf0 = $bs->translate(-frame=>0);
$orf1 = $bs->translate(-frame=>1);

# should output MNVN orf that starts in frame 0, not M* orf that starts in frame 1
$orf = $bs->translate(-orf=>1, -start=> 'atg');
if ($orf0->seq eq $orf->seq) {
        print "PASS";
}
else {
    print $orf0->seq . " != " . $orf->seq . "\n";
}

Gmane