[med-svn] [Git][med-team/kleborate][upstream] New upstream version 2.0.1

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / kleborate


Commits:
03f5f01d by Nilesh Patra at 2020-12-09T01:14:44+05:30
New upstream version 2.0.1
- - - - -


3 changed files:

- kleborate/data/CARD_AMR_clustered.csv
- kleborate/kaptive.py
- kleborate/version.py


Changes:

=====================================
kleborate/data/CARD_AMR_clustered.csv
=====================================
@@ -1568,8 +1568,7 @@ clusterid,queryID,class,gene,allele,seqID,accession,positions,size,cluster_conta
 135,SHV-107,Bla,SHV-OKP-LEN,SHV-107,1568,ARO_3001156,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR
 135,SHV-26,Bla,SHV-OKP-LEN,SHV-26,1569,ARO_3001084,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_chr
 135,SHV-49,Bla,SHV-OKP-LEN,SHV-49,1570,ARO_3001106,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR
-135,SHV-56.v1,Bla,SHV-OKP-LEN,SHV-56.v1,1571,ARG_AY352599,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_ESBL
-135,SHV-56.v2,Bla,SHV-OKP-LEN,SHV-56.v2,1572,ARO_3001112,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR
+135,SHV-56,Bla,SHV-OKP-LEN,SHV-56,1572,ARO_3001112,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR
 135,SHV-72,Bla,SHV-OKP-LEN,SHV-72,1573,ARO_3001126,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR
 135,SHV-110,Bla,SHV-OKP-LEN,SHV-110,1574,ARO_3001159,-,-,no,no,class A extended-spectrum beta-lactamase,Bla_chr
 135,SHV-145,Bla,SHV-OKP-LEN,SHV-145,1575,ARO_3001185,-,-,no,no,class A extended-spectrum beta-lactamase,Bla_chr


=====================================
kleborate/kaptive.py
=====================================
@@ -70,7 +70,7 @@ def run_kaptive(kaptive_py, kaptive_db, contigs, output_file, one_thread):
         kaptive_prefix = tmp_dir + '/kaptive'
         kaptive_table = kaptive_prefix + '_table.txt'
 
-        p = subprocess.Popen('python3 ' + kaptive_py +
+        p = subprocess.Popen(sys.executable + ' ' + kaptive_py +
                              ' -a ' + contigs +
                              ' -k ' + kaptive_db +
                              ' -o ' + kaptive_prefix +


=====================================
kleborate/version.py
=====================================
@@ -16,4 +16,4 @@ not, see <http://www.gnu.org/licenses/>.
 """
 
 
-__version__ = '2.0.0'
+__version__ = '2.0.1'



View it on GitLab: https://salsa.debian.org/med-team/kleborate/-/commit/03f5f01d11be02c4cc36f8c9870fb964118af4b3

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View it on GitLab: https://salsa.debian.org/med-team/kleborate/-/commit/03f5f01d11be02c4cc36f8c9870fb964118af4b3
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