[med-svn] [Git][med-team/parsnp][master] 7 commits: routine-update: New upstream version
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Mon Jul 11 21:09:20 BST 2022
Étienne Mollier pushed to branch master at Debian Med / parsnp
Commits:
39cc1ea8 by Étienne Mollier at 2022-07-11T21:57:03+02:00
routine-update: New upstream version
- - - - -
bfc0d9b7 by Étienne Mollier at 2022-07-11T21:57:14+02:00
New upstream version 1.7.4+dfsg
- - - - -
29df196f by Étienne Mollier at 2022-07-11T21:57:14+02:00
Update upstream source from tag 'upstream/1.7.4+dfsg'
Update to upstream version '1.7.4+dfsg'
with Debian dir 19e9af097c558d8716e23d8981b4ed9315eb88d7
- - - - -
746df1df by Étienne Mollier at 2022-07-11T21:57:18+02:00
Remove duplicate line from changelog.
Changes-By: lintian-brush
- - - - -
c260a080 by Étienne Mollier at 2022-07-11T21:58:37+02:00
Refresh py3-parsnp-libs.patch.
- - - - -
16b72e42 by Étienne Mollier at 2022-07-11T21:59:29+02:00
ready to upload to unstable
- - - - -
56b9cc13 by Étienne Mollier at 2022-07-11T22:08:47+02:00
d/control: ah, don't forget to remove abpoa.
Gbp-Dch: ignore
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/py3-parsnp-libs.patch
- extend.py
- parsnp
Changes:
=====================================
debian/changelog
=====================================
@@ -1,14 +1,12 @@
-parsnp (1.7.3+dfsg-1) UNRELEASED; urgency=medium
+parsnp (1.7.4+dfsg-1) unstable; urgency=medium
-TODO: wait for abpoa to pass through NEW.
- * d/control: add myself to uploaders.
* New upstream version
+ * d/control: add myself to uploaders.
* Standards-Version: 4.6.1 (routine-update)
* Delete typos.patch: applied upstream.
* Refresh proper_calls_to_tools.patch and py3-parsnp-libs.patch.
- * d/control: add dependency to python3-pyabpoa.
- -- Étienne Mollier <emollier at debian.org> Sat, 09 Jul 2022 21:10:31 +0200
+ -- Étienne Mollier <emollier at debian.org> Mon, 11 Jul 2022 21:57:03 +0200
parsnp (1.7.2+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -7,7 +7,6 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all-dev,
- python3-pyabpoa,
python3-setuptools,
cython3,
libmuscle-dev
=====================================
debian/patches/py3-parsnp-libs.patch
=====================================
@@ -14,9 +14,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
from Bio.AlignIO.MauveIO import MauveWriter, MauveIterator
-from logger import logger
+from parsnp.logger import logger
- import pyabpoa as pa
import time
#%%
+
--- parsnp.orig/parsnp
+++ parsnp/parsnp
@@ -8,7 +8,7 @@
@@ -35,5 +35,5 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
-import extend as ext
+import parsnp.extend as ext
- __version__ = "1.7.3"
+ __version__ = "1.7.4"
reroot_tree = True #use --midpoint-reroot
=====================================
extend.py
=====================================
@@ -15,7 +15,6 @@ import numpy as np
from Bio.AlignIO.MafIO import MafWriter, MafIterator
from Bio.AlignIO.MauveIO import MauveWriter, MauveIterator
from logger import logger
-import pyabpoa as pa
import time
#%%
@@ -306,7 +305,7 @@ def write_extended_xmfa(
cluster_idx = int(msa_record._annotations["pass"])
(record_matches, record_maxmatches), _ = get_ani_cutoff([record.seq for record in msa_record])
old_matches, old_max_matches = record_matches + old_matches, record_maxmatches + old_max_matches
- old_nucs_aligned += sum(len(record.seq) for record in msa_record)
+ old_nucs_aligned += sum(len(str(record.seq).replace("-", "")) for record in msa_record)
for direction in ("right", "left"):
expand_by = clusterdir_expand[(cluster_idx, direction)]
flanks = []
@@ -355,23 +354,20 @@ def write_extended_xmfa(
empty_seqs = [i for i in range(len(seqlist)) if seqlist[i] == ""]
nonempty_seqs = [s for s in seqlist if s != ""]
msa_result_temp = []
- if minlen < 50:
- aligner = pa.msa_aligner()
- # time.sleep(.25)
- res = aligner.msa(nonempty_seqs, out_cons=False, out_msa=True)
- msa_result_temp = res.msa_seq
- else:
+ if len(nonempty_seqs) > 1:
nonempty_seq_file = f"{cluster_directory}/cluster{cluster_idx}_{direction}_nonempty.fa"
SeqIO.write(
(SeqIO.SeqRecord(Seq(sequence), id=str(seq_idx)) for seq_idx, sequence in enumerate(nonempty_seqs)),
nonempty_seq_file,
"fasta")
subprocess.check_call(
- f"muscle -super5 {nonempty_seq_file} -output {nonempty_seq_file}_aligned.fa -threads {cpu_count}",
+ f"mafft --thread {cpu_count} {nonempty_seq_file} > {nonempty_seq_file}_aligned.fa",
stdout=subprocess.DEVNULL,
stderr=subprocess.STDOUT,
shell=True)
msa_result_temp = [str(record.seq) for record in SeqIO.parse(f"{nonempty_seq_file}_aligned.fa", "fasta")]
+ else:
+ msa_result_temp = nonempty_seqs
msa_result = []
idx = 0
for aligned_seq in msa_result_temp:
@@ -423,7 +419,7 @@ def write_extended_xmfa(
msa_record.annotations["cluster"] = cluster_idx
(record_matches, record_maxmatches), _ = get_ani_cutoff([record.seq for record in msa_record])
new_matches, new_max_matches = record_matches + new_matches, record_maxmatches + new_max_matches
- new_nucs_aligned += sum(len(record.seq) for record in msa_record)
+ new_nucs_aligned += sum(len(str(record.seq).replace("-", "")) for record in msa_record)
write_xmfa_cluster(extended_maf_file, [msa_record], fname_header_to_gcontigidx)
# maf_writer.write_alignment(msa_record)
total_length = sum(l for l in fname_contigid_to_length.values())
=====================================
parsnp
=====================================
@@ -19,7 +19,7 @@ from glob import glob
import extend as ext
-__version__ = "1.7.3"
+__version__ = "1.7.4"
reroot_tree = True #use --midpoint-reroot
try:
View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/compare/3fc5e10fe70df8b2eff8ac33253e3f479a738f93...56b9cc13d1b2147ae9a8a24c19b6bb3efaf0bf54
--
View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/compare/3fc5e10fe70df8b2eff8ac33253e3f479a738f93...56b9cc13d1b2147ae9a8a24c19b6bb3efaf0bf54
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