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

[Chris Fields]

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.
> _______________________________________________
> 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. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign