[med-svn] [Git][med-team/parsnp][upstream] New upstream version 1.5.6+dfsg

[Nilesh Patra (@nilesh)]

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
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