From 7ba7c5fe8be5cf116013fe9be7cf933ca52aeba4 Mon Sep 17 00:00:00 2001 From: Haibao Tang Date: Wed, 27 Sep 2023 00:41:33 -0700 Subject: [PATCH] minor --- goatools/anno/annoreader_base.py | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/goatools/anno/annoreader_base.py b/goatools/anno/annoreader_base.py index 84cc9d4..1eb79fb 100755 --- a/goatools/anno/annoreader_base.py +++ b/goatools/anno/annoreader_base.py @@ -36,8 +36,7 @@ class AnnoReaderBase(object): ) valid_formats = {"gpad", "gaf", "gene2go", "id2gos"} - - exp_nss = set(["BP", "MF", "CC"]) + exp_nss = {"BP", "MF", "CC"} def __init__(self, name, filename=None, **kws): # kws: allow_missing_symbol @@ -46,15 +45,10 @@ def __init__(self, name, filename=None, **kws): self.godag = kws.get("godag") self.namespaces = kws.get("namespaces") self.evobj = EvidenceCodes() - # Read anotation file, store namedtuples: - # Gene2GoReader(filename=None, taxids=None): - # GafReader(filename=None, hdr_only=False, prt=sys.stdout, allow_missing_symbol=False): - # GpadReader(filename=None, hdr_only=False): self.hdr = None self.datobj = None # pylint: disable=no-member self.associations = self._init_associations(filename, **kws) - # assert self.associations, 'NO ANNOTATIONS FOUND: {ANNO}'.format(ANNO=filename) assert self.namespaces is None or isinstance(self.namespaces, set) def get_desc(self):