[med-svn] [Git][med-team/parsnp][master] 6 commits: New upstream version 2.0.1+dfsg
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Jan 18 19:11:22 GMT 2024
Étienne Mollier pushed to branch master at Debian Med / parsnp
Commits:
8e9efa97 by Étienne Mollier at 2024-01-18T20:04:11+01:00
New upstream version 2.0.1+dfsg
- - - - -
b939cb2f by Étienne Mollier at 2024-01-18T20:04:11+01:00
routine-update: New upstream version
- - - - -
73d737dc by Étienne Mollier at 2024-01-18T20:04:12+01:00
Update upstream source from tag 'upstream/2.0.1+dfsg'
Update to upstream version '2.0.1+dfsg'
with Debian dir 5c6907d06c22c2e5de46fbb69937dcd745f409d6
- - - - -
069e70d2 by Étienne Mollier at 2024-01-18T20:07:38+01:00
proper_calls_to_tools.patch: refresh.
- - - - -
8ced5b28 by Étienne Mollier at 2024-01-18T20:07:46+01:00
py3-parsnp-libs.patch: refresh.
- - - - -
2640df35 by Étienne Mollier at 2024-01-18T20:09:48+01:00
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/patches/proper_calls_to_tools.patch
- debian/patches/py3-parsnp-libs.patch
- parsnp
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+parsnp (2.0.1+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 18 Jan 2024 20:07:57 +0100
+
parsnp (2.0.0+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/patches/proper_calls_to_tools.patch
=====================================
@@ -14,7 +14,7 @@ Forwarded: not-needed
run_command(command,1, prepend_time=True)
os.chdir(currdir)
-@@ -644,7 +644,7 @@
+@@ -646,7 +646,7 @@
missing = True
logger.critical("{} not in system path!".format(exe))
if use_phipack:
@@ -23,7 +23,7 @@ Forwarded: not-needed
if shutil.which(exe) is None:
missing = True
logger.critical("{} not in system path!".format(exe))
-@@ -659,7 +659,7 @@
+@@ -661,7 +661,7 @@
logger.critical("No fasttree executable found in system path!".format(exe))
missing = missing or (not has_fasttree)
else:
@@ -32,7 +32,7 @@ Forwarded: not-needed
if shutil.which(exe) is None:
missing = True
logger.critical("{} not in system path!".format(exe))
-@@ -971,7 +971,7 @@
+@@ -973,7 +973,7 @@
logger.debug("Writing .ini file")
if xtrafast or 1:
args.extend = False
@@ -41,7 +41,7 @@ Forwarded: not-needed
inifiled = inifiled.replace("$REF", ref)
inifiled = inifiled.replace("$EXTEND", "%d" % (args.extend))
inifiled = inifiled.replace("$ANCHORS", str(args.min_anchor_length))
-@@ -1070,7 +1070,7 @@
+@@ -1072,7 +1072,7 @@
if not os.path.exists(inifile):
logger.error("ini file %s does not exist!\n"%(inifile))
sys.exit(1)
@@ -50,7 +50,7 @@ Forwarded: not-needed
# with open(f"{outputDir}/parsnpAligner.out", 'w') as stdout_f, open(f"{outputDir}/parsnpAligner.err", 'w') as stderr_f:
# rc = run_command(command, ignorerc=1, stdout=stdout_f, stderr=stderr_f, prepend_time=True)
rc = run_logged_command(command=command, ignorerc=1, label="parsnp-aligner", outputDir=outputDir)
-@@ -1291,10 +1291,10 @@
+@@ -1293,10 +1293,10 @@
logger.info("Recruiting genomes...")
if use_parsnp_mumi:
if not inifile_exists:
@@ -63,7 +63,7 @@ Forwarded: not-needed
run_logged_command(command=command, outputDir=outputDir, label="parsnp-mumi")
# Takes eeach sequence and computes its mumi distance to the reference
try:
-@@ -1746,7 +1746,7 @@
+@@ -1748,7 +1748,7 @@
break
if not use_fasttree:
with TemporaryDirectory() as raxml_output_dir:
=====================================
debian/patches/py3-parsnp-libs.patch
=====================================
@@ -28,12 +28,12 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
import multiprocessing
import argparse
import signal
-@@ -25,7 +25,7 @@
- from random import shuffle
+@@ -24,7 +24,7 @@
+ from pathlib import Path
-import extend as ext
+import parsnp.extend as ext
from tqdm import tqdm
- __version__ = "2.0.0"
+ __version__ = "2.0.1"
=====================================
parsnp
=====================================
@@ -22,14 +22,14 @@ from multiprocessing import Pool
from Bio import SeqIO
from glob import glob
from pathlib import Path
-from random import shuffle
import extend as ext
from tqdm import tqdm
-__version__ = "2.0.0"
+__version__ = "2.0.1"
reroot_tree = True #use --midpoint-reroot
+random_seeded = random.Random(42)
try:
import dendropy
@@ -203,7 +203,9 @@ def parallelPhiWrapper(params):
def run_logged_command(command, outputDir, label, **kwargs):
with open(f"{outputDir}/log/{label}.out", 'w') as stdout_f, open(f"{outputDir}/log/{label}.err", 'w') as stderr_f:
- return run_command(command="time " + command, stdout=stdout_f, stderr=stderr_f, **kwargs)
+ if shutil.which("time") is not None:
+ command = "time " + command
+ return run_command(command=command, stdout=stdout_f, stderr=stderr_f, **kwargs)
def run_command(command, ignorerc=0, stdout=subprocess.PIPE, stderr=subprocess.PIPE):
global SIGINT
@@ -1220,7 +1222,7 @@ SETTINGS:
reflen = 0
if ref == "!":
- ref = random.choice(input_files)
+ ref = random_seeded.choice(input_files)
# Check if reference genome is aligned
reflen = check_ref_genome_aligned(ref)
@@ -1318,7 +1320,7 @@ SETTINGS:
ref = auto_ref
lowest_mumi = mumi_dict[idx]
mumi_f = ""
- if mumi_only and not curated:
+ if mumi_only:
mumi_f = open(os.path.join(outputDir, "config", "recruited_genomes.lst"),'w')
@@ -1348,6 +1350,9 @@ SETTINGS:
mumi_f.write(os.path.abspath(fnafiles[idx])+",%f"%(mumi_dict[idx])+"\n")
finalfiles.append(fnafiles[idx])
allfiles.append(fnafiles[idx])
+ if mumi_only:
+ mumi_f.close()
+ exit(0)
else:
try:
@@ -1412,10 +1417,6 @@ SETTINGS:
if f not in allfiles:
allfiles.append(f)
- if mumi_only:
- mumi_f.close()
- sys.exit(1)
-
# More stuff to autopick the reference if needed:
orig_auto_ref = auto_ref
if os.path.exists(auto_ref) and autopick_ref:
@@ -1442,6 +1443,7 @@ SETTINGS:
ffo.close()
ref = auto_ref
+ finalfiles = sorted(finalfiles)
totseqs = len(finalfiles)
#initiate parallelPhiPack tasks
@@ -1612,7 +1614,7 @@ SETTINGS:
full_query_list_path = f"{outputDir}/config/input-list.txt"
with open(full_query_list_path, 'w') as input_list_handle:
- shuffle(finalfiles)
+ random_seeded.shuffle(finalfiles)
for qf in finalfiles:
input_list_handle.write(qf + "\n")
@@ -1649,7 +1651,7 @@ SETTINGS:
logger.error(f"Partition {cl} failed...")
good_chunks.remove(cl)
- chunk_labels = list(good_chunks)
+ chunk_labels = sorted(list(good_chunks))
logger.info("Computing intersection of all partition LCBs...")
chunk_to_intvervaldict = partition.get_chunked_intervals(partition_output_dir, chunk_labels)
View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/compare/afae2ba45b934b07245e93175e027dd90c5dccab...2640df35ceb3a87b7ebcec04c1eaed165b61912c
--
View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/compare/afae2ba45b934b07245e93175e027dd90c5dccab...2640df35ceb3a87b7ebcec04c1eaed165b61912c
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