[Bioperl-l] RE: [Bioperl-guts-l] [Bug 1600] New:
$gb->species->ncbi_taxid
Brian Osborne
brian_osborne at cognia.com
Fri Mar 12 14:49:17 EST 2004
James,
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.
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?
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
>//
>
>
>
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