Changeset 1716:4c4266f7c5a5 in orange-bioinformatics


Ignore:
Timestamp:
08/30/12 16:05:10 (20 months ago)
Author:
markotoplak
Branch:
default
Message:

Removed the old version of obiKEGG. Renamed obiKEGG2 -> obiKEGG.

Location:
_bioinformatics
Files:
8 edited
12 moved

Legend:

Unmodified
Added
Removed
  • _bioinformatics/obiGO.py

    r1712 r1716  
    629629            available = sf.listfiles("GO") 
    630630            if file not in available: 
    631                 from . import obiKEGG2 
    632                 raise obiKEGG2.OrganismNotFoundError(org + str(code)) 
     631                from . import obiKEGG 
     632                raise obiKEGG.OrganismNotFoundError(org + str(code)) 
    633633            orngServerFiles.download("GO", file) 
    634634 
  • _bioinformatics/obiGene.py

    r1715 r1716  
    66 
    77from . import obiTaxonomy 
     8from . import obiKEGG 
    89 
    910default_database_path = orngServerFiles.localpath("NCBI_geneinfo") 
     
    648649 
    649650    def _organism_name(self, organism): 
    650         from . import obiKEGG2 
    651         return obiKEGG2.organism_name_search(organism) 
     651        return obiKEGG.organism_name_search(organism) 
    652652 
    653653    def create_aliases(self): 
    654654        organism = self._organism_name(self.organism) 
    655         from . import obiKEGG2 
    656         org = obiKEGG2.KEGGOrganism(self.organism, genematcher=GMDirect()) 
     655        org = obiKEGG.KEGGOrganism(self.organism, genematcher=GMDirect()) 
    657656        osets = org._gm_gene_aliases() 
    658657        return osets 
    659658 
    660659    def create_aliases_version(self): 
    661         from . import obiKEGG2 
    662         return obiKEGG2.KEGGOrganism.organism_version(self.organism) + ".1" 
     660        return obiKEGG.KEGGOrganism.organism_version(self.organism) + ".1" 
    663661 
    664662    def filename(self): 
  • _bioinformatics/obiGeneSets.py

    r1713 r1716  
    4545    Returns gene sets from KEGG pathways. 
    4646    """ 
    47     from . import obiKEGG2 as obiKEGG 
    4847     
    4948    kegg = obiKEGG.KEGGOrganism(org) 
     
    7877    Return gene sets from miRNA targets 
    7978    """ 
    80     from . import obimiRNA, obiKEGG2 
    81     org_code = obiKEGG2.from_taxid(org) 
     79    from . import obimiRNA 
     80    org_code = obiKEGG.from_taxid(org) 
    8281    link_fmt = "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=%s" 
    8382    mirnas = [(id, obimiRNA.get_info(id)) for id in obimiRNA.ids(org_code)] 
     
    350349    """ 
    351350    orngServerFiles.update_local_files() 
    352  
    353     from . import obiKEGG2 as obiKEGG 
    354351 
    355352    genesetsfn = [ keggGeneSets, goGeneSets, miRNAGeneSets] 
  • _bioinformatics/obiGenomicsUpdate.py

    r1636 r1716  
    198198        pkgUpdate.UpdateAnnotation(org) 
    199199 
    200     pkgUpdate = obiGenomicsUpdate.PKGUpdate("kegg", obiKEGG.Update()) 
    201  
    202     print "Updating KEGG taxonomy" 
    203     pkgUpdate.UpdateTaxonomy() 
    204  
    205     print "Updating KEGG orthology" 
    206     pkgUpdate.UpdateOrthology() 
    207  
    208     print "Updating KEGG reference pathways" 
    209     pkgUpdate.UpdateReference() 
    210  
    211     for org, name in [("hsa", "Homo sapiens"), ("sce", "Yeast")]: 
    212         print "Updating KEGG pathways for", name 
    213         pkgUpdate.UpdateOrganism(org) 
    214      
    215  
    216200def firstUpdateQt(): 
    217201    pass 
  • _bioinformatics/obiKEGG/__init__.py

    r1715 r1716  
    2020from datetime import datetime 
    2121 
    22 from Orange.utils import lru_cache, serverfiles 
     22from Orange.utils import lru_cache 
    2323 
    2424from . import databases 
     
    223223        info = genome.api.binfo(name) 
    224224        return info.release 
    225 #        orngServerFiles.localpath_download("KEGG", "kegg_genes_%s.tar.gz" % name) 
    226 #        return orngServerFiles.info("KEGG", "kegg_genes_%s.tar.gz" % name)["datetime"] 
    227225     
    228226    def _set_genematcher(self, genematcher): 
  • _bioinformatics/obiKEGG/api.py

    r1636 r1716  
    348348        touch_dir(path) 
    349349        return caching.Sqlite3Store(os.path.join(path, 
    350                                                  "kegg_api_cache.sqlite3")) 
     350                                                 "kegg_api_cache_1.sqlite3")) 
    351351     
    352352    def last_modified(self, args, kwargs=None): 
  • _bioinformatics/obiPPI.py

    r1682 r1716  
    1616 
    1717from . import obiTaxonomy 
    18 from .obiKEGG import downloader 
     18 
    1919from .obiTaxonomy import pickled_cache 
    2020 
  • _bioinformatics/obiTaxonomy.py

    r1715 r1716  
    333333    """ See if the code is a valid code in any database and return a set of its taxids. 
    334334    """ 
    335     from . import obiKEGG2, obiGO 
     335    from . import obiKEGG, obiGO 
    336336    results = set() 
    337     for test in [obiKEGG2.to_taxid, obiGO.to_taxid]: 
     337    for test in [obiKEGG.to_taxid, obiGO.to_taxid]: 
    338338        try: 
    339339            r = test(code) 
  • _bioinformatics/obimiRNA.py

    r1715 r1716  
    77import statc 
    88 
    9 from . import obiGene as ge, obiGO as go, obiKEGG2 as kg, obiProb as op, obiTaxonomy 
     9from . import obiGene as ge, obiGO as go, obiKEGG as kg, obiProb as op, obiTaxonomy 
    1010 
    1111mirnafile = osf.localpath_download('miRNA','miRNA.txt') 
     
    188188                 
    189189        else: 
    190             from . import obiKEGG2 
    191             raise obiKEGG2.OrganismNotFoundError(taxid) 
     190            from . import obiKEGG 
     191            raise obiKEGG.OrganismNotFoundError(taxid) 
    192192         
    193193class mat_miRNA: 
  • _bioinformatics/widgets/OWKEGGPathwayBrowser.py

    r1715 r1716  
    2323 
    2424from .. import obiTaxonomy 
    25 from .. import obiKEGG2 as obiKEGG 
     25from .. import obiKEGG 
    2626from .. import obiGeneSets 
    2727 
     
    727727         
    728728    def ClearCache(self): 
    729         from ..obiKEGG2 import caching 
     729        from ..obiKEGG import caching 
    730730        try: 
    731731            caching.clear_cache() 
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