[Bioperl-l] Re: [Bioperl-guts-l] [Bug 1600] New:
$gb->species->ncbi_taxid
James Wasmuth
james.wasmuth at ed.ac.uk
Sat Mar 13 10:34:01 EST 2004
Brian,
>Yes, I could read your patch but I'm lazy. You said:
>
>
>>>create a Bio::Species object, but the genus=unknown species=marine
>>>
>>>
>subspecies=gamma.
>
I was highlighting the problem my patch would create. I hadn't thought
too hard about its consequences, but realise that it may have some
knock-on effects.
>
>Shouldn't the values be the same for all these "species" for which the genus
>is not known? Like:
>
>Genus=unknown, species=unknown, subspecies=unknown
>
>That way you can check, since one can no longer use "unless defined
>$species_object" to see if real species information is lacking or not. Have
>I missed something here?
>
NCBI taxonomy considers the term 'unknown marine gamma proteobacterium
NOR5' to represent a species, though for this example there remaining
taxonomy classification is awarded no rank until 'class'.
So one possible fix, would be:
if (ORGANISM ne "synonym for taxid 32644") {
then add rest of name into $species.
}
therefore $genus = unknown and $species = marine gamma proteobacterium NOR5
other problems are organisms such as "leaf litter basidiomycete sp.
Collb2-39". Currently $genus = leaf, $species = litter and $subsp =
basidiomycete. Perhaps $subsp should contain everything left over?
Thoughts? Also does anyone know off hand if it copes with 'varietas'
and 'var.' for plants? I expect not. I will have a look at the
genbank.pm on Monday and suggest a patch. I expect these issues will
also be pertinent in embl.pm and other database format modules...
hmmmm, anyone with thoughts?
-james
>
>Brian O.
>
>
>-----Original Message-----
>From: James Wasmuth [mailto:james.wasmuth at ed.ac.uk]
>Sent: Thursday, March 11, 2004 9:40 AM
>To: Brian Osborne
>Cc: bioperl-guts-l at bioperl.org
>Subject: Re: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid
>
>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=42247
>&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.
>>_______________________________________________
>>Bioperl-guts-l mailing list
>>Bioperl-guts-l at portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l
>>
>>
>>
>>
>>
>>
>
>--
>"I have not failed. I've just found 10,000 ways that don't work."
> --- Thomas Edison
>
>Nematode Bioinformatics ||
>Blaxter Nematode Genomics Group ||
>School of Biological Sciences ||
>Ashworth Laboratories ||
>King's Buildings || tel: +44 131 650 7403
>University of Edinburgh || web: www.nematodes.org
>Edinburgh ||
>EH9 3JT ||
>UK ||
>
>
>
>
More information about the Bioperl-l
mailing list