[Bioperl-l] Re: [Bioperl-guts-l] [Bug 1600] New:
$gb->species->ncbi_taxid
Heikki Lehvaslaiho
heikki at ebi.ac.uk
Thu Mar 11 10:06:10 EST 2004
James,
I think you are on the right track here. Getting the taxid and the higher
taxa is more important than the lack of binomial name.
I am moving this discussion from guts into bioperl-l list where it belongs.
Thank your your contribution. Putting a patch into bugzilla as an attachment
is exactly the right thing to do.
-Heikki
On Thursday 11 Mar 2004 14:39, James Wasmuth wrote:
> Brian and all at bioperl-guts,
>
>
> below is the comment I've added to the bug[1600]. I think it may need
> some discussion, but the patch I've added works to the extent that it
> allows creation of a Bio::Species object but the subsequent genus,
> species, subspecies calls will be 'wrong'. Personally I'm more
> concerned with the taxid, which I think will be sufficient.
>
> If you want to see the size of this problem go to NCBI taxonomy and
> enter the term identified as a token set! I think that maintaining the
> taxid is enough, otherwise the artifical split of terms such as
> **unidentified diatom endosymbiont of Peridinium foliaceum*
> <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4224
>7&lvl=3&lin=f&keep=1&srchmode=3&unlock>* may be a problem, though some of
> them are intuitive.
>
> One last question, I've never tried to fix a bug before, so I've
> commited a patch as an attachment to Bugzilla for the bug. Do others
> check this and if okay place it in the code...
> apologies for the newbie bit...
>
> -james
>
>
>
> genbank.pm
>
> line 1123: return unless $genus and $genus !~ /^(Unknown|None)$/oi;
>
> a number of species are described as Unknown blah blah blah.
>
> The NCBI taxid assigned to unknown taxa is 32644 and has a number of
> synonyms, none of which are 'unknown'.
>
> The list includes: other, unknown organism, not specified, not shown,
> unspecified, Unknown, None, unclassified , unidentified organism
>
> I've changed the _read_GenBank_Species subroutine to allow organism
> names such as 'unknown marine gamma proteobacterium NOR5'. This will
> create a Bio::Species object, but the genus=unknown species=marine
> subspecies=gamma.
>
> There is a whole host of species names that ignore the nice rules in
> _read_GenBank_Species! However this fix will allow the correct taxid to
> be provided which I think is more than the name!
>
>
>
> sub _read_GenBank_Species {
> my( $self,$buffer) = @_;
> my @organell_names = ("chloroplast", "mitochondr");
> # only those carrying DNA, apart from the nucleus
>
> #CHANGE
> my @unkn_names=("other", 'unknown organism', 'not specified', 'not
> shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified
> organism');
>
> $_ = $$buffer;
>
> my( $sub_species, $species, $genus, $common, $organelle, @class,
> $ns_name );
> # upon first entering the loop, we must not read a new line -- the
> SOURCE
> # line is already in the buffer (HL 05/10/2000)
> while (defined($_) || defined($_ = $self->_readline())) {
> # de-HTMLify (links that may be encountered here don't contain
> # escaped '>', so a simple-minded approach suffices)
> s/<[^>]+>//g;
> if (/^SOURCE\s+(.*)/o) {
> # FIXME this is probably mostly wrong (e.g., it yields things like
> # Homo sapiens adult placenta cDNA to mRNA
> # which is certainly not what you want)
> $common = $1;
> $common =~ s/\.$//; # remove trailing dot
> } elsif (/^\s{2}ORGANISM/o) {
> my @spflds = split(' ', $_);
> ($ns_name) = $_ =~ /\w+\s+(.*)/o;
> shift(@spflds); # ORGANISM
>
> if(grep { $_ =~ /^$spflds[0]/i; } @organell_names) {
> $organelle = shift(@spflds);
> }
> $genus = shift(@spflds);
> if(@spflds) {
> $species = shift(@spflds);
> } elsif ( grep { $genus } @unkn_names){
> $species = '';
> } else {$species='sp.';} #there's no species name but it
> isn't unclassified
> $sub_species = shift(@spflds) if(@spflds);
> } elsif (/^\s+(.+)/o) {
> # only split on ';' or '.' so that
> # classification that is 2 words will
> # still get matched
> # use map to remove trailing/leading spaces
> push(@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/,
> $1);
> } else {
> last;
> }
>
> $_ = undef; # Empty $_ to trigger read of next line
> }
>
> $$buffer = $_;
>
> # Don't make a species object if it's empty or "Unknown" or "None"
> my $unkn = grep { $_ =~ /^$genus$species/i; } @unkn_names;
>
> return unless $genus and $unkn==0;
>
> # Bio::Species array needs array in Species -> Kingdom direction
> if ($class[0] eq 'Viruses') {
> push( @class, $ns_name );
> }
> elsif ($class[$#class] eq $genus) {
> push( @class, $species );
> } else {
> push( @class, $genus, $species );
> }
> @class = reverse @class;
>
> my $make = Bio::Species->new();
> $make->classification( \@class, "FORCE" ); # no name validation please
> $make->common_name( $common ) if $common;
> unless ($class[-1] eq 'Viruses') {
> $make->sub_species( $sub_species ) if $sub_species;
> }
> $make->organelle($organelle) if $organelle;
> return $make;
> }
>
> Brian Osborne wrote:
> >James,
> >
> >Your guess is right, no Species is made because of the name. That's
> > because genbank.pm normally looks at:
> >
> >ORGANISM Bos taurus
> >
> >And makes "Bos" the genus, and so on.
> >
> >If it sees:
> >
> >ORGANISM Unknown
> >
> >It refuses to make a Species object, and it's interpreting your ORGANISM
> >line in the same way because it can't make a valid genus, that's the
> > current rule. Personally I'd say that I agree with its principle - how
> > can we make a Species object without genus and species?
> >
> >You can get the taxid from a SeqFeature object, you already knew that.
> >
> >Brian O.
> >
> >
> >-----Original Message-----
> >From: bioperl-guts-l-bounces at portal.open-bio.org
> >[mailto:bioperl-guts-l-bounces at portal.open-bio.org]On Behalf Of
> >bugzilla-daemon at portal.open-bio.org
> >Sent: Thursday, March 11, 2004 4:21 AM
> >To: bioperl-guts-l at bioperl.org
> >Subject: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid
> >
> >http://bugzilla.bioperl.org/show_bug.cgi?id=1600
> >
> > Summary: $gb->species->ncbi_taxid
> > Product: Bioperl
> > Version: unspecified
> > Platform: PC
> > OS/Version: Linux
> > Status: NEW
> > Severity: normal
> > Priority: P2
> > Component: Bio::SeqIO
> > AssignedTo: bioperl-guts-l at bioperl.org
> > ReportedBy: james.wasmuth at ed.ac.uk
> >
> >
> >I've included a genbank file for which I have been unable to extract the
> >ncbi_taxid for using
> >
> >$gb->species->ncbi_taxid
> >
> >the error is:
> >Can't call method "ncbi_taxid" on an undefined value
> >
> >infact I don't get a Bio::Species object. I'm sure its because of the
> > name, which is correct.
> >
> >I've tried looking into it, but could not find which Seq object creates
> > the Bio::Species object.
> >
> >
> >
> >LOCUS AY007676 1389 bp DNA linear BCT
> >29-OCT-2001
> >DEFINITION Unknown marine gamma proteobacterium NOR5 16S ribosomal RNA,
> > partial sequence.
> >ACCESSION AY007676
> >VERSION AY007676.1 GI:12000362
> >KEYWORDS .
> >SOURCE unknown marine gamma proteobacterium NOR5
> > ORGANISM unknown marine gamma proteobacterium NOR5
> > Bacteria; Proteobacteria; Gammaproteobacteria.
> >REFERENCE 1 (bases 1 to 1389)
> > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., Gerdts,G.
> >and
> > Amann,R.
> > TITLE Isolation of novel pelagic bacteria from the German bight and
> >their
> > seasonal contributions to surface picoplankton
> > JOURNAL Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001)
> > MEDLINE 21536174
> > PUBMED 11679337
> >REFERENCE 2 (bases 1 to 1389)
> > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O.,
> > Gerdts,G., Schuett,C. and Amann,R.
> > TITLE Identification and seasonal dominance of culturable marine
> >bacteria
> > JOURNAL Unpublished
> >REFERENCE 3 (bases 1 to 1389)
> > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O.,
> > Gerdts,G., Schuett,C. and Amann,R.
> > TITLE Direct Submission
> > JOURNAL Submitted (29-AUG-2000) Molecular Ecology,
> > Max-Planck-Institute, Celsiusstrasse 1, Bremen 28359, Germany
> >FEATURES Location/Qualifiers
> > source 1..1389
> > /organism="unknown marine gamma proteobacterium NOR5"
> > /mol_type="genomic DNA"
> > /db_xref="taxon:145658"
> > rRNA <1..>1389
> > /product="16S ribosomal RNA"
> >BASE COUNT 343 a 319 c 453 g 274 t
> >ORIGIN
> > 1 cgcgaaagta cttcggtatg agtagagcgg cggacgggtg agtaacgcgt
> > aggaatctat 61 ccagtagtgg gggacaactc ggggaaactc gagctaatac cgcatacgtc
> > ctaagggaga 121 aagcggggga tcttcggacc tcgcgctatt ggaggagcct gcgttggatt
> > agctagttgg 181 tggggtaaag gcctaccaag gcgacgatcc atagctggtc tgagaggatg
> > atcagccaca 241 ccgggactga gacacggccc ggactcctac gggaggcagc agtggggaat
> > attgcgcaat 301 gggcgaaagc ctgacgcagc catgccgcgt gtgtgaagaa ggccttcggg
> > ttgtaaagca 361 ctttcaattg ggaagaaagg ttagtagtta ataactgcta gctgtgacat
> > tacctttaga 421 agaagcaccg gctaactccg tgccagcagc cgcggtaata cggaggtgcg
> > agcgttaatc 481 ggaattactg ggcgtaaagc gcgcgtaggc ggtctgttaa gtcggatgtg
> > aaagccccgg 541 gctcaacctg ggaattgcac ccgatactgg ccgactggag tgcgagagag
> > ggaggtagaa 601 ttccacgtgt agcggtgaaa tgcgtagata tgtggaggaa taccggtggc
> > gaaggcggcc 661 tcctggctcg acactgacgc tgaggtgcga aagcgtgggg agcaaacagg
> > attagatacc 721 ctggtagtcc acgccgtaaa cgatgtctac tagccgttgg gagacttgat
> > ttcttggtgg 781 cgaagttaac gcgataagta gaccgcctgg ggagtacggc cgcaaggtta
> > aaactcaaat 841 gaattgacgg gggcccgcac aagcggtgga gcatgtggtt taattcgatg
> > caacgcgaag 901 aaccttacca ggccttgaca tcctaggaat cctgtagaga tacgggagtg
> > ccttcgggaa 961 tctagtgaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt
> > gggttaagtc 1021 ccgtaacgag cgcaaccctt gtccttagtt gccagcgcgt aatggcggga
> > actctaagga 1081 gactgccggt gacaaaccgg aggaaggtgg ggacgacgtc aagtcatcat
> > ggcccttacg 1141 gcctgggcta cacacgtgct acaatggaac gcacagaggg cagcaaaccc
> > gcgaggggga 1201 gcgaatccca caaaacgttt cgtagtccgg atcggagtct gcaactcgac
> > tccgtgaagt 1261 cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgttcccg
> > ggccttgtac 1321 acaccgcccg tcacaccatg ggagtgggtt gctccagaag tggttagcct
> > aaccttcggg 1381 agggcgatc
> >//
> >
> >
> >
> >------- You are receiving this mail because: -------
> >You are the assignee for the bug, or are watching the assignee.
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--
______ _/ _/_____________________________________________________
_/ _/ http://www.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk
_/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
_/ _/ _/ Wellcome Trust Genome Campus, Hinxton
_/ _/ _/ Cambs. CB10 1SD, United Kingdom
_/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________
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