From 6f0fb988cbc3d1f5386fd4ee67a73fae8005fb34 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 17 Aug 2020 17:32:11 -0400 Subject: [PATCH] Fix for changes in PubMLST url Related to https://github.com/sanger-pathogens/ariba/issues/304 --- ariba/pubmlst_getter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ariba/pubmlst_getter.py b/ariba/pubmlst_getter.py index 444f88e7..b46b7d80 100644 --- a/ariba/pubmlst_getter.py +++ b/ariba/pubmlst_getter.py @@ -105,7 +105,7 @@ def _download_profile_and_fastas(self, outdir, profile_url, fasta_urls): self._download_file(profile_url, profile_outfile) for fasta_url in fasta_urls: - outfile = os.path.join(outdir, fasta_url.split('/')[-1]) + outfile = "{0}.tfa".format(os.path.join(outdir, fasta_url.split('/')[-2])) self._download_file(fasta_url, outfile + '.tmp') PubmlstGetter._rename_seqs_in_fasta(outfile + '.tmp', outfile) os.unlink(outfile + '.tmp')