Changeset 1719:6e8861564778 in orange-bioinformatics for _bioinformatics/obiPPI.py


Ignore:
Timestamp:
08/31/12 14:09:46 (20 months ago)
Author:
markotoplak
Branch:
default
Message:

Fixed update scripts for MeSH, GO, HomoloGene, NCBI_geneinfo, OMIM, PPI. Moved wget to Orange.utils.

File:
1 edited

Legend:

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  • _bioinformatics/obiPPI.py

    r1716 r1719  
    1313 
    1414from Orange.orng import orngServerFiles 
    15 from Orange.utils import ConsoleProgressBar, lru_cache 
     15from Orange.utils import ConsoleProgressBar, lru_cache, wget 
    1616 
    1717from . import obiTaxonomy 
     
    313313          
    314314        """ 
    315         # TODO: synonyms_interactor can contain multiple synonyms 
    316         # (should create an indexed table of synonyms) 
     315            # TODO: synonyms_interactor can contain multiple synonyms 
     316            # (should create an indexed table of synonyms) 
    317317        if taxid is None: 
    318318            cur = self.db.execute("""\ 
     
    355355        filepath = orngServerFiles.localpath("PPI", "BIOGRID-ALL.tab2") 
    356356        cls.init_db(filepath) 
    357         shutil.remove(filepath) 
     357        os.remove(filepath) 
    358358         
    359359    @classmethod 
     
    367367        headers = lineiter.next() # read the first line 
    368368         
    369         con = sqlite3.connect(os.path.join(dirname, "BIOGRID-ALL.sqlite")) 
     369        con = sqlite3.connect(os.path.join(dirname, BioGRID.SERVER_FILE)) 
    370370        con.execute("drop table if exists links") # Drop old table 
    371371        con.execute("drop table if exists proteins") # Drop old table 
     
    445445from collections import namedtuple 
    446446from functools import partial 
    447  
    448 from .obiGeneMania import wget, copyfileobj 
    449447 
    450448def chainiter(iterable): 
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