[med-svn] [Git][med-team/parsnp][upstream] New upstream version 2.0.4+dfsg

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / parsnp


Commits:
efcf33fa by Étienne Mollier at 2024-03-17T09:56:27+01:00
New upstream version 2.0.4+dfsg
- - - - -


2 changed files:

- CITATION
- parsnp


Changes:

=====================================
CITATION
=====================================
@@ -1,9 +1,14 @@
-[Parsnp]
+[Parsnp 2]
+   Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ:
+     Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets. 
+     bioRxiv (2024). doi: https://doi.org/10.1101/2024.01.30.577458
 
+[Parsnp 1]
    Treangen TJ*, Ondov BD*, Koren S, Phillippy AM:
      The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
      Genome Biology (2014). doi: http://dx.doi.org/10.1186/s13059-014-0524-x
 
+
 * These authors contributed equally to this work
 
 External software (please also cite if you find Parsnp useful):


=====================================
parsnp
=====================================
@@ -25,7 +25,7 @@ from pathlib import Path
 import extend as ext
 from tqdm import tqdm
 
-__version__ = "2.0.3"
+__version__ = "2.0.4"
 reroot_tree = True #use --midpoint-reroot
 random_seeded = random.Random(42)
 
@@ -1402,7 +1402,7 @@ SETTINGS:
                         for line in results:
                             # FastANI results file -> Query, Ref, ANI val, extra stuff,,,
                             line = line.split('\t')
-                            if float(line[2]) >= min_ani_cutoff and (int(line[3]) / int(line[4])) * 100 > args.min_ref_cov:
+                            if float(line[2]) >= min_ani_cutoff and (int(line[3]) / int(line[4])) * 100 >= args.min_ref_cov:
                                 genome_to_genomes[line[1]].append(line[0])
 
                         ani_ref = max(genome_to_genomes, key=(lambda key: len(genome_to_genomes[key])))
@@ -1753,7 +1753,7 @@ SETTINGS:
                 command = "fasttree -nt -quote -gamma -slow -boot 100 "+outputDir+os.sep+"parsnp.snps.mblocks"
 
             run_logged_command(command, outputDir=outputDir, label="fasttree")
-
+            shutil.move(f"{outputDir}/log/fasttree.out", f"{outputDir}/parsnp.tree")
 
 
         #7)reroot to midpoint



View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/commit/efcf33fa3bf74f0ec110ceb199d6cdc5762d6f33

-- 
View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/commit/efcf33fa3bf74f0ec110ceb199d6cdc5762d6f33
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