def set_meta( self, dataset, **kwd ):
"""
for lped/pbed eg
"""
Html.set_meta( self, dataset, **kwd )
if kwd.get('overwrite') == False:
return True
try:
efp = dataset.extra_files_path
except:
return False
try:
flist = os.listdir(efp)
except:
return False
if len(flist) == 0:
return False
self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy Impute2 datatype object'
if not dataset.blurb:
dataset.blurb = 'Composite file - Otago Impute2 Galaxy toolkit'
return True
def set_meta( self, dataset, **kwd ):
"""
for lped/pbed eg
"""
Html.set_meta( self, dataset, **kwd )
if kwd.get('overwrite') == False:
if verbose:
gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False')
return True
try:
efp = dataset.extra_files_path
except:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
return False
try:
flist = os.listdir(efp)
except:
if verbose: gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name))
return False
if len(flist) == 0:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name,efp))
return False
self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy genotype datatype object'
if not dataset.blurb:
dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit'
return True
def set_meta( self, dataset, **kwd ):
"""
for lped/pbed eg
"""
Html.set_meta( self, dataset, **kwd )
if kwd.get('overwrite') == False:
if verbose:
gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False')
return True
try:
efp = dataset.extra_files_path
except:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
return False
try:
flist = os.listdir(efp)
except:
if verbose: gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name))
return False
if len(flist) == 0:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name,efp))
return False
self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy genotype datatype object'
if not dataset.blurb:
dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit'
return True
def set_meta(self, dataset, **kwd):
Html.set_meta(self, dataset, **kwd)
efp = dataset.extra_files_path
flist = os.listdir(efp)
for i, fname in enumerate(flist):
if fname.endswith('.grp'):
dataset.metadata.reference_name = fname[:-4]
break
self.regenerate_primary_file(dataset)
def set_meta(self, dataset, **kwd):
"""
NOTE we apply the tabular machinary to the phenodata extracted
from a BioC eSet or affybatch.
"""
Html.set_meta(self, dataset, **kwd)
try:
flist = os.listdir(dataset.extra_files_path)
except:
if verbose:
gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
return False
bn = dataset.metadata.base_name
if not bn:
for f in flist:
n = os.path.splitext(f)[0]
bn = n
dataset.metadata.base_name = bn
if not bn:
bn = '?'
dataset.metadata.base_name = bn
pn = '%s.pheno' % (bn)
pp = os.path.join(dataset.extra_files_path, pn)
dataset.metadata.pheno_path = pp
try:
pf = file(pp, 'r').readlines(
) # read the basename.phenodata in the extra_files_path
except:
pf = None
if pf:
h = pf[0].strip()
h = h.split('\t') # hope is header
h = [escape(x) for x in h]
dataset.metadata.column_names = h
dataset.metadata.columns = len(h)
dataset.peek = ''.join(pf[:5])
else:
dataset.metadata.column_names = []
dataset.metadata.columns = 0
dataset.peek = 'No pheno file found'
if pf and len(pf) > 1:
dataset.metadata.pheCols = self.get_phecols(phenolist=pf)
else:
dataset.metadata.pheCols = [
('', 'No useable phenotypes found', False),
]
#self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy Expression datatype object'
if not dataset.blurb:
dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit'
return True
def set_meta( self, dataset, **kwd ):
"""
NOTE we apply the tabular machinary to the phenodata extracted
from a BioC eSet or affybatch.
"""
Html.set_meta(self, dataset, **kwd)
try:
flist = os.listdir(dataset.extra_files_path)
except:
if verbose:
gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
return False
bn = dataset.metadata.base_name
if not bn:
for f in flist:
n = os.path.splitext(f)[0]
bn = n
dataset.metadata.base_name = bn
if not bn:
bn = '?'
dataset.metadata.base_name = bn
pn = '%s.pheno' % (bn)
pp = os.path.join(dataset.extra_files_path,pn)
dataset.metadata.pheno_path=pp
try:
pf = file(pp,'r').readlines() # read the basename.phenodata in the extra_files_path
except:
pf = None
if pf:
h = pf[0].strip()
h = h.split('\t') # hope is header
h = [escape(x) for x in h]
dataset.metadata.column_names = h
dataset.metadata.columns = len(h)
dataset.peek = ''.join(pf[:5])
else:
dataset.metadata.column_names = []
dataset.metadata.columns = 0
dataset.peek = 'No pheno file found'
if pf and len(pf) > 1:
dataset.metadata.pheCols = self.get_phecols(phenolist=pf)
else:
dataset.metadata.pheCols = [('','No useable phenotypes found',False),]
#self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy Expression datatype object'
if not dataset.blurb:
dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit'
return True
def set_meta( self, dataset, **kwd ):
Html.set_meta( self, dataset, **kwd )
self.regenerate_primary_file(dataset)
def set_meta( self, dataset, **kwd ):
log.debug("## set_meta for FusionInspector ")
Html.set_meta( self, dataset, **kwd )
self.regenerate_primary_file(dataset)
def set_meta(self, dataset, **kwd):
log.debug("## set_meta for FusionInspector ")
Html.set_meta(self, dataset, **kwd)
self.regenerate_primary_file(dataset)
