def getGroupMap(groups,taxonomy):
"""
Return map from all indicated taxids to True
input may be a taxid, taxon name, or file listing taxids
"""
if groups is None or len(groups)==0:
return None
taxidmap={}
for group in groups:
if os.path.isfile(group):
taxidmap.update(parseListToMap(group,keyType=int))
else:
taxon = getTaxonFromArg(taxonomy, group)
taxidmap.update( createTaxMap(taxon) )
return taxidmap
def screenRecords(stream, separatorRE, idRE=None, keep=False, screenMap=None, screenFile=None):
"""
uses recordIterator(strean, separatorRE, idRE) to parse input into records
uses screenMap (can be read from screenFile) to identify records
identified records are kept or skipped based on the value of keep
"""
if screenMap is None:
if screenFile is None:
raise Exception("Please supply a hash(Python map) or file of record keys")
else:
screenMap=parseListToMap(screenFile)
for (recordId, recordLines) in recordIterator(stream,separatorRE,idRE=idRE):
screened = recordId in screenMap
if screened == keep:
for line in recordLines:
yield line