def load_list(self,yml,filename):
# make a dict from the k/v pairs in yml where type(v) is a scalar (string or number)
scalars=scalar_values(yml)
scalars['filename']=filename
readset_objs=[]
errors=[]
rlist=yml['readsets']
if type(rlist) != type([]): # make sure rlist is a list
raise ConfigError("%s: type of 'readsets' must be a list; got '%s'" % (filename, type(rlist)))
for ryml in rlist:
if type(ryml)!=type({}): # make sure elements of rlist are dicts
raise ConfigError("%s: elements of readsets must be dicts (hashes); got '%s'" % (filename, type(ryml)))
ryml.update(scalars)
try:
rs=self.load_glob(ryml,filename)[0]
except ConfigError as ce:
errors.append(str(ce))
continue
rs.update(scalars)
readset_objs.append(rs)
if len(errors)>0:
raise ConfigError("%s:\n"%filename+"\n".join(errors))
return readset_objs
def load_glob(self,yml,filename):
try: reads_files=yml['reads_file']
except KeyError:
try: reads_files=yml['reads_files']
except KeyError: raise ConfigError("%s: readset does not define reads_file(s)" % filename)
# get the reads directory, if present
try: reads_dir=yml['reads_dir']
except KeyError: reads_dir=os.getcwd() # fixme: hope this is right thing to do
# hack?
reads_dir=evoque_template(reads_dir, RnaseqGlobals.config['rnaseq']) # in case of ${root_dir}
#print "lg: reads_dir is %s" % reads_dir
files=[]
globlist=re.split('[\s,]+',reads_files)
missing=[]
for fglob in globlist:
if not os.path.isabs(fglob):
fglob=os.path.normpath(os.path.join(reads_dir, fglob))
filelist=glob.glob(fglob)
if len(files)==0:
missing.append("%s: no matching files for %s" % (filename, fglob))
files.extend(filelist)
if len(files)==0:
msg=", ".join(missing)
raise ConfigError(msg)
# Make the Readset object:
#print "load_glob: files is %s" % files
scalars=scalar_values(yml)
scalars['filename']=filename
scalars['reads_files']=files
return [Readset(scalars)]
