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debian/changelog
View file @ bb677a4e
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@debian.org> Wed, 11 Dec 2019 15:20:13 +0100
-- Andreas Tille <tille@debian.org> Wed, 11 Dec 2019 17:08:14 +0100
srst2 (0.2.0-6) unstable; urgency=medium
......
debian/control
View file @ bb677a4e
......@@ -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
View file @ bb677a4e
......@@ -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
View file @ bb677a4e
......@@ -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
......