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

Martin MOKREJŠ mmokrejs at ribosome.natur.cuni.cz
Thu Aug 31 18:04:21 EDT 2006


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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