Andreas Tille pushed to branch master at Debian Med / kleborate
Commits:
e4516b86 by Andreas Tille at 2019-09-24T14:39:32Z
Recommends: python3-biopython to run additional scripts
- - - - -
845b8cf7 by Andreas Tille at 2019-09-24T14:44:04Z
Enhance patch for Python3 compatibility
- - - - -
2 changed files:
- debian/control
- debian/patches/python3.patch
Changes:
=====================================
debian/control
=====================================
@@ -18,8 +18,9 @@ Package: kleborate
Architecture: any
Depends: ${python3:Depends},
${misc:Depends},
- ncbi-blast+ <!nocheck>,
- mash <!nocheck>
+ ncbi-blast+,
+ mash
+Recommends: python3-biopython
Description: tool to screen Klebsiella genome assemblies
Kleborate is a tool to screen Klebsiella genome assemblies for:
.
=====================================
debian/patches/python3.patch
=====================================
@@ -1,5 +1,6 @@
Author: Andreas Tille <[email protected]>
Last-Update: Tue, 24 Sep 2019 12:36:03 +0200
+Origin: https://github.com/katholt/Kleborate/issues/17
Description: When using Python3 the executable is named python3
--- a/kleborate-runner.py
@@ -17,7 +18,7 @@ Description: When using Python3 the executable is named
python3
# If resistance genes are on, run the resBLAST.py script to get its
headers.
if args.resistance:
- res_out = subprocess.check_output('python ' + resblast +
-+ res_out = subprocess.check_output('python3 ' + resblast +
++ res_out = subprocess.check_output(sys.executable + ' ' +
resblast +
' -s ' + data_folder + '/ARGannot_r2.fasta' +
' -t ' + data_folder + '/ARGannot_clustered80_r2.csv',
shell=True)
@@ -26,7 +27,7 @@ Description: When using Python3 the executable is named
python3
kaptive_table = kaptive_prefix + '_table.txt'
- p = subprocess.Popen('python ' + kaptive_py +
-+ p = subprocess.Popen('python3 ' + kaptive_py +
++ p = subprocess.Popen(sys.executable + ' ' + kaptive_py +
' -a ' + contigs +
' -k ' + kaptive_db +
' -o ' + kaptive_prefix +
@@ -35,7 +36,7 @@ Description: When using Python3 the executable is named
python3
def get_chromosome_mlst_results(mlstblast, data_folder, contigs):
- f = os.popen('python ' + mlstblast +
-+ f = os.popen('python3 ' + mlstblast +
++ f = os.popen(sys.executable + ' ' + mlstblast +
' -s ' + data_folder +
'/Klebsiella_pneumoniae.fasta' +
' -d ' + data_folder + '/kpneumoniae.txt' +
' -i no' +
@@ -44,7 +45,7 @@ Description: When using Python3 the executable is named
python3
vir_name,
vir_st_name, unknown_group_name, min_gene_count,
header_function):
- f = os.popen('python ' + mlstblast +
-+ f = os.popen('python3 ' + mlstblast +
++ f = os.popen(sys.executable + ' ' + mlstblast +
' -s ' + data_folder + '/' + alleles_fasta +
' -d ' + data_folder + '/' + profiles_txt +
' -i yes' +
@@ -53,7 +54,7 @@ Description: When using Python3 the executable is named
python3
def get_hypermucoidy_results(rmpablast, data_folder, contigs):
hypermucoidy = '-'
- f = os.popen('python ' + rmpablast +
-+ f = os.popen('python3 ' + rmpablast +
++ f = os.popen(sys.executable + ' ' + rmpablast +
' -s ' + data_folder + '/hypermucoidy.fasta' +
' -d ' + data_folder +
'/hypermucoidy_rmpA.txt' +
' ' + contigs)
@@ -62,7 +63,7 @@ Description: When using Python3 the executable is named
python3
def get_wzi_and_k_locus_results(mlstblast, data_folder, contigs):
wzi_st, k_type = '-', '-'
- f = os.popen('python ' + mlstblast +
-+ f = os.popen('python3 ' + mlstblast +
++ f = os.popen(sys.executable + ' ' + mlstblast +
' -s ' + data_folder + '/wzi.fasta' +
' -d ' + data_folder + '/wzi.txt' +
' -i yes' +
@@ -71,7 +72,7 @@ Description: When using Python3 the executable is named
python3
res_hits = []
if args.resistance:
- f = os.popen('python ' + resblast +
-+ f = os.popen('python3 ' + resblast +
++ f = os.popen(sys.executable + ' ' + resblast +
' -s ' + data_folder +
'/ARGannot_r2.fasta' +
' -t ' + data_folder +
'/ARGannot_clustered80_r2.csv' +
' -q ' + data_folder + '/QRDR_120.aa' +
View it on GitLab:
https://salsa.debian.org/med-team/kleborate/compare/44ecf104d5ce95dd8e9b9633dd13eb9ce3a7d3e3...845b8cf7d51825c6c8568444993444dc78342cb0
--
View it on GitLab:
https://salsa.debian.org/med-team/kleborate/compare/44ecf104d5ce95dd8e9b9633dd13eb9ce3a7d3e3...845b8cf7d51825c6c8568444993444dc78342cb0
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