[Bioperl-l] Memory requirements for conversion from embl to genbank

Martin MOKREJŠ mmokrejs at ribosome.natur.cuni.cz
Fri Sep 1 03:24:06 EDT 2006


This problem did not appear with 1.5.1. I will contact the people for sure
next week.
M.

Chris Fields wrote:
> Yet another problem?!?  Martin, I'll ask this again, mainly out of 
> curiosity: have you ever contacted the people who generated this to  let
> them know of the problems?
> 
> This one is definitely not valid: can't have a lineage w/o an organism!
> 
> Chris
> 
> On Aug 31, 2006, at 5:04 PM, Martin MOKREJŠ wrote:
> 
>> Sendu,
>>   one more problem with the taxonomic code:
>>
>> ID   5MLE000012 standard; mRNA; VRL; 421 BP.
>> XX
>> AC   BB136482;
>> XX
>> DT   26-JUL-2001 (Rel. 15, Created)
>> DT   26-JUL-2001 (Rel. 15, Last updated, Version 1)
>> XX
>> DE   5'UTR in Murine leukemia virus Mo Ampho MCF recombinant gPr80 
>> envelope
>> DE   polyprotein (env) gene, complete cds.
>> XX
>> DR   EMBL; U36991;
>> DR   UTR; CC147674;
>> XX
>> OC   Viruses; Retro-transcribing viruses; Retroviridae; 
>> Orthoretrovirinae;
>> OC   Gammaretrovirus.
>> XX
>> UT   5'UTR;
>> XX
>> FH   Key             Location/Qualifiers
>> FH
>> FT   5'UTR           1..421
>> FT                   /source="EMBL::U36991:1..421"
>> FT                   /gene="env"
>> FT                   /product="gPr80 envelope polyprotein"
>> FT   VECTOR          1..132
>> FT                   /source="EMBL::U36991:1..132"
>> FT                   /evidence="Similarity"
>> FT                   /db_xref="EMBL:"
>> FT                   /note="Possible vector contamination"
>> FT                   /note="Length=133 BP. Identities=99.2%"
>> XX
>> SQ   Sequence 421 BP; 88 A; 142 C; 118 G; 73 T; 0 other;
>>      acttgtggtc tcgctgttcc ttgggagggt ctcctctgag tgattgacta 
>> ccgtcagcgg        60
>>      gggtctttca tttgggggct cgtccgggat cgggagaccc ctgcccaggg 
>> accaccgacc       120
>>      caccaccggg agctcactta caggcccttc aagcagtaca acgagaggtc 
>> tggaagccac       180
>>      tggctgcggc ctatcaggac cagcaagacc agccagtgat accacacccc 
>> ttccgtgtcg       240
>>      gcgacaccgt gtgggtacgc cggcaccaga ctaagaactt ggaacctcgt 
>> tggaaaggac       300
>>      cctataccgt cctgctgacc acccccaccg ctctcaaagt agacggcatc 
>> gctgcgtgga       360
>>      tccacgccgc tcacgtaaag gcggcgacaa cccctccggc cggaacagca 
>> tcaggaccga       420
>>      
>> c                                                                     
>>   421
>> //
>>
>>
>>
>> ------------- EXCEPTION  -------------
>> MSG: Must supply a Bio::Taxon
>> STACK Bio::DB::Taxonomy::list::ancestor /usr/lib/perl5/site_perl/
>> 5.8.8/Bio/DB/Taxonomy/list.pm:332
>> STACK Bio::Taxon::ancestor /usr/lib/perl5/site_perl/5.8.8/Bio/
>> Taxon.pm:476
>> STACK Bio::Tree::TreeFunctionsI::get_lineage_nodes /usr/lib/perl5/
>> site_perl/5.8.8/Bio/Tree/TreeFunctionsI.pm:197
>> STACK Bio::Tree::Tree::new /usr/lib/perl5/site_perl/5.8.8/Bio/Tree/
>> Tree.pm:112
>> STACK Bio::Species::classification /usr/lib/perl5/site_perl/5.8.8/
>> Bio/Species.pm:182
>> STACK Bio::SeqIO::embl::_read_EMBL_Species /usr/lib/perl5/site_perl/
>> 5.8.8/Bio/SeqIO/embl.pm:1094
>> STACK Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.8/Bio/
>> SeqIO/embl.pm:330
>> STACK toplevel testparsing.pl:22
>>
>> --------------------------------------
>>
>> I guess the 'OS' line missing caused that.
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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> 
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> 

-- 
Dr. Martin Mokrejs
Faculty of Science, Charles University
Vinicna 5, 128 43 Prague, Czech Republic
http://www.iresite.org
http://www.iresite.org/~mmokrejs


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