Nilesh Patra pushed to branch upstream at Debian Med / parsnp
Commits: 7c256597 by Nilesh Patra at 2021-05-31T02:42:55+05:30 New upstream version 1.5.6+dfsg - - - - - 2 changed files: - README.md - parsnp Changes: ===================================== README.md ===================================== @@ -6,7 +6,11 @@ Parsnp is a command-line-tool for efficient microbial core genome alignment and # Installation - +## From conda +Parsnp is available on the [Bioconda](https://bioconda.github.io/user/install.html#set-up-channels) channel. This is the recommended method of installation and can be installed via +``` +conda install parsnp +``` ## From source ===================================== parsnp ===================================== @@ -14,7 +14,7 @@ import signal import inspect from multiprocessing import * -__version__ = "1.5.4" +__version__ = "1.5.6" reroot_tree = True #use --midpoint-reroot try: @@ -475,6 +475,10 @@ def parse_args(): "--use-fasttree", action = "store_true", help = "Use fasttree instead of RaxML") + misc_args.add_argument( + "--vcf", + action = "store_true", + help = "Generate VCF file.") misc_args.add_argument( "-p", "--threads", @@ -583,6 +587,7 @@ if __name__ == "__main__": genbank_ref = "" reflen = 0 use_gingr = "" + generate_vcf = args.vcf filtreps = False repfile = "" @@ -759,9 +764,10 @@ if __name__ == "__main__": logger.critical("No seqs provided, yet required. exit!") sys.exit(0) # TODO Should this exit value be 0? elif not ref and query: - logger.warning("No reference genome specified, going to autopick from %s as closest to %s\n"%(seqdir, query)) + logger.warning("No reference genome specified, going to autopick from input as closest to %s\n"%(query)) autopick_ref = True ref = query + print("Ref", ref) logger.info(""" {} @@ -1357,6 +1363,8 @@ Please verify recruited genomes are all strain of interest""") run_command("harvesttools -q -b %s,REP,\"Intragenomic repeats > 100bp\" -o %s/parsnp.ggr -i %s/parsnp.ggr"%(repfile,outputDir,outputDir)) run_command("harvesttools -q -i %s/parsnp.ggr -S "%(outputDir)+outputDir+os.sep+"parsnp.snps.mblocks") + if generate_vcf: + run_command("harvesttools -q -i %s/parsnp.ggr -V "%(outputDir)+outputDir+os.sep+"parsnp.vcf") logger.info("Reconstructing core genome phylogeny...") with open(os.path.join(outputDir, "parsnp.snps.mblocks")) as mblocks: @@ -1477,6 +1485,8 @@ Please verify recruited genomes are all strain of interest""") if not VERBOSE and os.path.exists("%s/all_mumi.ini"%(outputDir)): os.remove("%s/all_mumi.ini"%(outputDir)) + if not VERBOSE and os.path.exists("%s/tmp"%(outputDir)): + shutil.rmtree("%s/tmp"%(outputDir)) if os.path.exists("%s/parsnp.snps.mblocks"%(outputDir)): os.remove("%s/parsnp.snps.mblocks"%(outputDir)) View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/commit/7c25659759eea63c0bf0042cd126a07d577fac25 -- View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/commit/7c25659759eea63c0bf0042cd126a07d577fac25 You're receiving this email because of your account on salsa.debian.org.
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