[Bioperl-l] EMBL format field

Chris Fields cjfields at uiuc.edu
Sun Jun 15 01:17:10 EDT 2008


Um, should have attached a link there:

http://www.bioperl.org/wiki/FAQ#I_am_using_Ensembl.__How_do_I_do_XYZ.3F

chris

On Jun 14, 2008, at 9:25 PM, Chris Fields wrote:

> See this FAQ question, as well as the one following it.
>
> chris
>
> On Jun 14, 2008, at 8:39 AM, Zhi-Qiang Ye wrote:
>
>> Thank all of you.  I finally get the newest version of bioperl
>> installed and solved the problem.
>>
>> I noticed that ensembl API still uses bioperl-1.2.3, which
>> misleaded me that bioperl-1.4 is very up-to-date ...
>>
>>
>> Regards,
>> Zhi-Qiang
>>
>>
>> 2008/6/12 Kevin Brown <Kevin.M.Brown at asu.edu>:
>>> See the following links for where to get a more current version.   
>>> 1.4 is
>>> years old and lots of parts are non-functional due to website and  
>>> file
>>> format changes.
>>>
>>> http://www.bioperl.org/wiki/Installing_BioPerl
>>>
>>> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>>>> Zhi-Qiang Ye
>>>> Sent: Thursday, June 12, 2008 2:07 AM
>>>> To: Jason Stajich
>>>> Cc: bioperl list
>>>> Subject: Re: [Bioperl-l] EMBL format field
>>>>
>>>> Hi, Jason
>>>>
>>>>  I used exactly your code, and the result is still 'unknown id'.
>>>> Where can I get the version of bioperl?
>>>> I used ubuntu gutsy, the version in ubuntu's package
>>>> management system is 1.4-1.
>>>>
>>>>  I installed BioPerl 1.4 on another computer, IA64 with redhat
>>>> linux.  It has the same problem.
>>>> In the process of installation using CPAN, make test always  
>>>> failed. So
>>>> I used 'force install ....'.
>>>> I am not sure it is the reason.
>>>>
>>>> Thanks.
>>>> Zhi-Qiang Ye
>>>>
>>>> 2008/6/11 Jason Stajich <jason at bioperl.org>:
>>>>> What version of bioperl? It works for me using  this code I
>>>> get 'CB271253'
>>>>> printed out.
>>>>>
>>>>> #!/usr/bin/perl -w
>>>>> use strict;
>>>>> use Bio::SeqIO;
>>>>> my $in = Bio::SeqIO->new(-format => 'embl', -file => shift);
>>>>> while( my $seq = $in->next_seq ) {
>>>>> print $seq->id,"\n";
>>>>> }
>>>>>
>>>>> On Jun 10, 2008, at 4:43 AM, Zhi-Qiang Ye wrote:
>>>>>
>>>>>> That's weird. I also met this problem. I tried a
>>>> embl-format file like
>>>>>> this:
>>>>>>
>>>>>> ID   CB271253; SV 1; linear; mRNA; EST; INV; 591 BP.
>>>>>> XX
>>>>>> AC   CB271253;
>>>>>> XX
>>>>>> DT   24-FEB-2003 (Rel. 74, Created)
>>>>>> DT   24-FEB-2003 (Rel. 74, Last updated, Version 1)
>>>>>> XX
>>>>>> DE   taa17c02.x2 Hydra EST -II Hydra magnipapillata cDNA
>>>> 3' similar to
>>>>>> DE   SW:OPSD_RABIT P49912 RHODOPSIN. ;, mRNA sequence.
>>>>>>
>>>>>> from:
>>>> http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=CB271253&style=raw
>>>>>>
>>>>>> the $seq object's   ->id, ->display_id  are "unkown id" ...
>>>>>>
>>>>>>
>>>>>>
>>>>>> ZQ Ye
>>>>>>
>>>>>> 2008/6/9 Hilmar Lapp <hlapp at gmx.net>:
>>>>>>>
>>>>>>> If this is the case with the latest version of BioPerl it
>>>> should be filed
>>>>>>> as
>>>>>>> a bug report for the embl parser. The ID ought to be reported in
>>>>>>> $seq->get_secondary_accessions() (which returns an
>>>> array). If it doesn't,
>>>>>>> it
>>>>>>> sounds like a bug to me.
>>>>>>>
>>>>>>>   -hilmar
>>>>>>>
>>>>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>>>>>
>>>>>>>> Hi Wen,
>>>>>>>> A dump of that sequence object (Data::Dumper is your
>>>> friend !) reveals
>>>>>>>> that the PA EMBL field is not saved into the object.
>>>> However, you will
>>>>>>>> find the string 'AB000170.1' in the embedded CDS
>>>> feature, more precisely
>>>>>>>> the seqid of the location object. I don't know whether
>>>> that is always
>>>>>>>> the case, but it is in your particular example.
>>>>>>>> So, to get your hands on that value you have to do:
>>>>>>>>
>>>>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'}
>>>> $seq->get_SeqFeatures;
>>>>>>>> my $parent_id = $cds->location->seq_id;
>>>>>>>>
>>>>>>>> HTH,
>>>>>>>> Marc
>>>>>>>>
>>>>>>>> Marc Logghe
>>>>>>>> Senior Bioinformatician
>>>>>>>> Ablynx nv
>>>>>>>>>
>>>>>>>>> -----Original Message-----
>>>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>>>>
>>>>>>>>> ###file###
>>>>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>>>>> XX
>>>>>>>>> PA   AB000170.1
>>>>>>>>> XX
>>>>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>>>>> XX
>>>>>>>>> OS   Sus scrofa (pig)
>>>>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata;
>>>> Vertebrata; Euteleostomi;
>>>>>>>>> Mammalia;
>>>>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina;
>>>> Suidae; Sus.
>>>>>>>>> OX   NCBI_TaxID=9823;
>>>>>>>>> .........
>>>>>>>>>
>>>>>>>>> I want the accession number in the line that starts
>>>> with PA, AB000170
>>>>>>>>> in this example.
>>>>>>>>>
>>>>>>>>> Can anybody kindly help, tell me which module and
>>>> method I should use?
>>>>>>>>> I tried various things like $seq_obj -> primary_id,  
>>>>>>>>> display_id,
>>>>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>>>>
>>>>>>>>> Thanks a lot!
>>>>>>>>>
>>>>>>>>> Wen
>>>>>>>>> _______________________________________________
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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