Ticket #353 (closed bug: fixed)

Opened 6 years ago

Last modified 6 years ago

obiGO in sgd GO

Reported by: blaz Owned by: ales
Milestone: Future Component: orng_modules
Severity: minor Keywords:
Cc: Blocking:
Blocked By:

Description

medtem ko spodnje dela:

>>> gsets = obiGeneSets.collections([":go:sce"])
Found annotations for Saccharomyces cerevisiae (sgd)

vrne

>>> gsets = obiGeneSets.collections([":go:sgd"])

napako (kar je cudno, ker, kot poroca sama funkcija, je pravo ime ravno "sgd").

In [20]: gsets = obiGeneSets.collections([":go:sgd"])
Unable to find annotations for 'None' Matching name against NCBI Taxonomy
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/blaz/Documents/Workspace/annotations/src/<ipython console> in <module>()

/Users/blaz/Documents/Workspace/Bioinformatics/obiGeneSets.py in collections(l, default, path)
    263     #pair in choosen are (name, location)
    264 
--> 265     return createCollection(list(choosen))
    266 
    267 """

/Users/blaz/Documents/Workspace/Bioinformatics/obiGeneSets.py in createCollection(lnf)
    179 
    180             elif name == "go":
--> 181                 gen2 = goGeneSets(keggToGo(org))
    182                 gen2 = prettyfygo(gen2)
    183                 gen1.update(addSource(gen2, ""))

/Users/blaz/Documents/Workspace/Bioinformatics/obiGeneSets.py in goGeneSets(goorg)
     24 
     25     ontology = obiGO.Ontology.Load()
---> 26     annotations = obiGO.Annotations.Load(goorg, ontology=ontology)
     27 
     28     terms = ontology.terms.keys()

/Users/blaz/Documents/Workspace/Bioinformatics/obiGO.py in Load(cls, org, ontology, progressCallback)
    501             print >> sys.stderr, "Unable to find annotations for", "'%s'" % org, "Matching name against NCBI Taxonomy"
    502             import obiTaxonomy as tax
--> 503             ids = tax.search(org)
    504             ids = set(ids).intersection(Taxonomy().tax.keys())
    505         codes = reduce(set.union, [from_taxid(id) for id in ids], set())

/Users/blaz/Documents/Workspace/Bioinformatics/obiTaxonomy.py in search(string, onlySpecies)
    243             - *onlySpecies* Return only taxids of species (and subspecies)
    244     """
--> 245     return Taxonomy().search(string, onlySpecies)
    246 
    247 def lineage(taxid):

/Users/blaz/Documents/Workspace/Bioinformatics/obiTaxonomy.py in search(self, string, onlySpecies)
    145 
    146     def search(self, string, onlySpecies=True):
--> 147         res = self._text.search(string)
    148         if onlySpecies:
    149             res = [r for r in res if "species" in self._text[r][1]]

/Users/blaz/Documents/Workspace/Bioinformatics/obiTaxonomy.py in search(self, string)
     81 
     82     def search(self, string):
---> 83         string = string.lower()
     84         res = []
     85         for idx in self._find_all(string):

AttributeError: 'NoneType' object has no attribute 'lower'

Change History

comment:1 Changed 6 years ago by anonymous

  • Status changed from new to closed
  • Resolution set to fixed
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