FastMLST
FastMLST copied to clipboard
patch for Pandas warnings with newer Pandas versions
--- mlst.py 2023-04-06 20:38:09.323863921 +0000
+++ mlst.py 2023-04-06 20:37:46.011441012 +0000
@@ -158,10 +158,10 @@
return None
else:
dfblast = dfblast.join(
- dfblast['sseqid'].str.split('.', 1, expand=True).
+ dfblast['sseqid'].str.split(pat='.', n=1, expand=True).
rename(columns={0: 'scheme', 1: 'genenumber'}))
dfblast = dfblast.join(
- dfblast['genenumber'].str.rsplit('_', 1, expand=True).
+ dfblast['genenumber'].str.rsplit(pat='_', n=1, expand=True).
rename(columns={0: 'gene', 1: 'number'}))
dfblast = dfblast.drop(['sseqid', 'genenumber'], axis=1)
dfblast['genome_id'] = self.beautiname
@@ -362,7 +362,7 @@
exit()
# check completeness, perfect identity, snp identity,
rank_list = defaultdict(dict)
- for scheme, group in self.blast.groupby(['scheme']):
+ for scheme, group in self.blast.groupby('scheme'):
rank_list[scheme] = defaultdict(dict)
rank_list[scheme]['score'] = 0
rank_list[scheme]['scheme'] = defaultdict()