[med-svn] [Git][med-team/srst2][master] 5 commits: Adapt to new interface of mock
Andreas Tille
gitlab at salsa.debian.org
Wed Dec 11 16:12:07 GMT 2019
Andreas Tille pushed to branch master at Debian Med / srst2
Commits:
747c946a by Andreas Tille at 2019-12-11T15:28:36Z
Adapt to new interface of mock
- - - - -
699e2a9e by Andreas Tille at 2019-12-11T15:43:29Z
Remove __pycache__ dirs from installation
- - - - -
b32c61fd by Andreas Tille at 2019-12-11T16:05:05Z
Fix spacing
- - - - -
4bd5c7ae by Andreas Tille at 2019-12-11T16:07:42Z
Fix some remaining interpreters
- - - - -
bb677a4e by Andreas Tille at 2019-12-11T16:10:36Z
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/2to3.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-srst2 (0.2.0-7) UNRELEASED; urgency=medium
+srst2 (0.2.0-7) unstable; urgency=medium
* Use 2to3 to port from Python2 to Python3
Closes: #938560
@@ -8,47 +8,8 @@ srst2 (0.2.0-7) UNRELEASED; urgency=medium
* autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
* Set upstream metadata fields: Repository, Repository-Browse.
* Use markdown instead of python-markdown
-
- TODO:
-cd tests && python3 test_slurm_srst2.py && python3 test_srst2.py
-...........
-----------------------------------------------------------------------
-Ran 11 tests in 0.024s
-
-OK
-...........EE....
-======================================================================
-ERROR: test_get_pileup_with_defaults (__main__.TestMPileup)
-----------------------------------------------------------------------
-Traceback (most recent call last):
- File "/usr/lib/python3/dist-packages/mock/mock.py", line 1330, in patched
- return func(*args, **keywargs)
- File "test_srst2.py", line 294, in test_get_pileup_with_defaults
- 'bowtie_sam_mod', 'fasta', 'pileup')
- File "/build/srst2-0.2.0/scripts/srst2.py", line 735, in get_pileup
- if args.threads > 1 and samtools_v1:
-TypeError: '>' not supported between instances of 'MagicMock' and 'int'
-
-======================================================================
-ERROR: test_get_pileup_with_overides (__main__.TestMPileup)
-----------------------------------------------------------------------
-Traceback (most recent call last):
- File "/usr/lib/python3/dist-packages/mock/mock.py", line 1330, in patched
- return func(*args, **keywargs)
- File "test_srst2.py", line 242, in test_get_pileup_with_overides
- 'bowtie_sam_mod', 'fasta', 'pileup')
- File "/build/srst2-0.2.0/scripts/srst2.py", line 735, in get_pileup
- if args.threads > 1 and samtools_v1:
-TypeError: '>' not supported between instances of 'MagicMock' and 'int'
-
-----------------------------------------------------------------------
-Ran 17 tests in 0.042s
-
-FAILED (errors=2)
-make[1]: *** [debian/rules:34: override_dh_auto_test] Error 1
-
-
- -- Andreas Tille <tille at debian.org> Wed, 11 Dec 2019 15:20:13 +0100
+
+ -- Andreas Tille <tille at debian.org> Wed, 11 Dec 2019 17:08:14 +0100
srst2 (0.2.0-6) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
dh-python,
- python3-all,
+ python3,
python3-setuptools,
markdown,
dos2unix,
=====================================
debian/patches/2to3.patch
=====================================
@@ -119,17 +119,83 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
+python3 csv_to_gene_db.py -t Clostridium_cdhit90.csv -o Clostridium_VF_clustered.fasta -s 5
--- a/database_clustering/align_plot_tree_min3.py
+++ b/database_clustering/align_plot_tree_min3.py
-@@ -14,7 +14,7 @@ for f in os.listdir(fasta_directory):
- if not f.startswith("."):
+@@ -11,44 +11,44 @@ fasta_directory = "/home/UNIMELB/hdashno
+ # Get the filenames of all files in the input directory "fasta_directory"
+ files = []
+ for f in os.listdir(fasta_directory):
+- if not f.startswith("."):
++ if not f.startswith("."):
if f.endswith(".fsa") or f.endswith(".fasta"):
- files.append('"'+os.path.join(fasta_directory,f)+'"') # need to surround with " " due to () in filenames
+- files.append('"'+os.path.join(fasta_directory,f)+'"') # need to surround with " " due to () in filenames
-print "Number of input files:", len(files)
++ files.append('"'+os.path.join(fasta_directory,f)+'"') # need to surround with " " due to () in filenames
+print("Number of input files:", len(files))
# Run muscle on each fasta file to produce an alignment for each
# Save the alignment file names so that they can be used in R ape
+ for f in files:
+- outfilename = (f+".aln").replace("(","").replace(")","")
+- #print outfilename
++ outfilename = (f+".aln").replace("(","").replace(")","")
++ #print outfilename
+ alignment = MuscleCommandline(input=f, out=outfilename)
+- #alignment()
++ #alignment()
+
+
+ r('''
+- require(ape, quietly=TRUE)
++ require(ape, quietly=TRUE)
+
+- all_files = list.files("/home/UNIMELB/hdashnow/resistance_database/by_gene",
++ all_files = list.files("/home/UNIMELB/hdashnow/resistance_database/by_gene",
+ pattern="aln$", full.names=TRUE)
+
+- pdf(width=9,height=12,file="trees.pdf")
++ pdf(width=9,height=12,file="trees.pdf")
+
+- for (filename in all_files) {
+- #print(filename)
+- aln = read.dna(filename, format="fasta")
+- if (dim(aln)[1] >= 3) {
++ for (filename in all_files) {
++ #print(filename)
++ aln = read.dna(filename, format="fasta")
++ if (dim(aln)[1] >= 3) {
+ d = dist(aln)
+- #print(aln)
+- tree=nj(d)
+- plot(tree, cex=0.6)
++ #print(aln)
++ tree=nj(d)
++ plot(tree, cex=0.6)
+ #print(filename)
+- min_filename = tail(strsplit(filename,"/")[[1]],1) # This needs to be made robust
+- #print(min_filename)
+- gene_name = strsplit(min_filename,"\\\.")[[1]][1]
+- #print(cluster)
+- title(paste("Gene: ", gene_name))
+- #dev.off()
++ min_filename = tail(strsplit(filename,"/")[[1]],1) # This needs to be made robust
++ #print(min_filename)
++ gene_name = strsplit(min_filename,"\\\.")[[1]][1]
++ #print(cluster)
++ title(paste("Gene: ", gene_name))
++ #dev.off()
+ }
+- }
+- dev.off()
++ }
++ dev.off()
+ ''')
--- a/database_clustering/csv_to_gene_db.py
+++ b/database_clustering/csv_to_gene_db.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+ # take csv table detailing clustering etc and sequences for gene DB, write as fasta
+ # expected csv file format:
+ # seqID,clusterid,gene,allele,(DNAseq),other....
@@ -45,18 +45,18 @@ if __name__ == "__main__":
if options.output_file == "":
DoError("Please specify output fasta file using -o")
@@ -603,6 +669,15 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
if args.other:
x = args.other
+@@ -732,7 +732,7 @@ def get_pileup(args, mapping_files_pre,
+ logging.info('Generate and sort BAM file...')
+ out_file_bam = mapping_files_pre + ".unsorted.bam"
+ view_command = [samtools_exec, 'view']
+- if args.threads > 1 and samtools_v1:
++ if args.threads.call_count > 1 and samtools_v1:
+ view_command += ['-@', str(args.threads)]
+ view_command += ['-b', '-o', out_file_bam, '-q', str(args.mapq), '-S', bowtie_sam_mod]
+ run_command(view_command)
@@ -806,12 +806,12 @@ def calculate_ST(allele_scores, ST_db, g
try:
clean_st = ST_db[allele_string]
@@ -773,3 +848,19 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'scripts')))
+--- a/database_clustering/VFDB_cdhit_to_csv.py
++++ b/database_clustering/VFDB_cdhit_to_csv.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+ '''
+ Created on 19/06/2013
+ @author: Harriet Dashnow, Kat Holt
+--- a/database_clustering/VFDBgenus.py
++++ b/database_clustering/VFDBgenus.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+ '''
+ Extract virulence genes by genus from the VFDB database at http://www.mgc.ac.cn/VFs/Down/CP_VFs.ffn.gz
+ '''
=====================================
debian/rules
=====================================
@@ -19,6 +19,7 @@ override_dh_install:
# fix line endings to make sure Python3 interpreter will be found
find debian/*/usr/share -name "VFDB*" -exec dos2unix \{\} \;
sed -i '1s:^#!/usr/local.*python[.0-9]*$$:#!/usr/bin/python3:' debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/qsub_srst2.py
+ find debian -name __pycache__ -type d | xargs rm -rf
override_dh_fixperms:
dh_fixperms
View it on GitLab: https://salsa.debian.org/med-team/srst2/compare/7ea98208ce2f4b5fb2c3237f49d4e6cacfa170d8...bb677a4e51b328d985454f5cd29a0e724a41b8f2
--
View it on GitLab: https://salsa.debian.org/med-team/srst2/compare/7ea98208ce2f4b5fb2c3237f49d4e6cacfa170d8...bb677a4e51b328d985454f5cd29a0e724a41b8f2
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