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Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 20 Apr 2016 10:31:32 +0200
Description: Fix path to Debian installed tools
Parsnp uses an unusual way to call external tools.
At first these are linked to some place relative to the scrip
location which is definitely not allowed on /usr in a Debian
installation. Later these symlinks are used for calling the tools.
.
This patch calls the according tools directly at their Debian
locations (and the Debian names).
--- a/Parsnp.py
+++ b/Parsnp.py
@@ -102,14 +102,14 @@ signal.signal(signal.SIGINT, handler)
def run_phipack(query,seqlen,workingdir):
currdir = os.getcwd()
os.chdir(workingdir)
- command = "%s/phiprofile -o -v -n %d -w 100 -m 100 -f %s > %s.out"%(PARSNP_DIR,seqlen,query,query)
+ command = "/usr/bin/phipack-profile -o -v -n %d -w 100 -m 100 -f %s > %s.out"%(seqlen,query,query)
run_command(command,1)
os.chdir(currdir)
def run_fasttree(query,workingdir,recombination_sites):
currdir = os.getcwd()
os.chdir(workingdir)
- command = "%s/ft -nt -quote -gamma -slow -boot 100 seq.fna > out.tree"%(PARSNP_DIR)
+ command = "fasttree -nt -quote -gamma -slow -boot 100 seq.fna > out.tree"
run_command(command,1)
os.chdir(currdir)
@@ -207,20 +207,6 @@ sys.stderr.write( BOLDME+"|--Parsnp %s--
sys.stderr.write( BOLDME+"For detailed documentation please see --> http://harvest.readthedocs.org/en/latest\n"+ENDC)
-if not os.path.lexists("%s/parsnp"%(PARSNP_DIR)):
- os.system("ln -s %s/bin/parsnp %s/parsnp"%(PARSNP_DIR, PARSNP_DIR))
-if not os.path.lexists("%s/harvest"%(PARSNP_DIR)):
- os.system("ln -s %s/bin/harvest_%s %s/harvest"%(PARSNP_DIR,binary_type,PARSNP_DIR))
-if not os.path.lexists("%s/ft"%(PARSNP_DIR)):
- os.system("ln -s %s/bin/fasttree_%s %s/ft"%(PARSNP_DIR,binary_type,PARSNP_DIR))
-if not os.path.lexists("%s/phiprofile"%(PARSNP_DIR)):
- os.system("ln -s %s/bin/Profile_%s %s/phiprofile"%(PARSNP_DIR,binary_type,PARSNP_DIR))
-
-if not os.path.lexists("%s/nucmer"%(PARSNP_DIR)):
- os.system("ln -s %s/MUMmer/nucmer %s/nucmer"%(PARSNP_DIR,PARSNP_DIR))
-if not os.path.lexists("%s/show-coords"%(PARSNP_DIR)):
- os.system("ln -s %s/MUMmer/show-coords %s/show-coords"%(PARSNP_DIR,PARSNP_DIR))
-
#set MUMmer paths
if os.path.exists("%s/MUMmer/nucmer_run"%(PARSNP_DIR)):
ff = open("%s/MUMmer/nucmer_run"%(PARSNP_DIR))
@@ -784,12 +770,12 @@ if __name__ == "__main__":
if use_parsnp_mumi and not curated:
sys.stderr.write( "-->Calculating MUMi..\n")
if not inifile_exists:
- command = "%s/parsnp %sall_mumi.ini"%(PARSNP_DIR,outputDir+os.sep)
+ command = "/usr/lib/parsnp/parsnp %sall_mumi.ini"%(outputDir+os.sep)
else:
if not os.path.exists(inifile):
sys.stderr.write( "Error: ini file %s does not exist!\n"%(inifile))
sys.exit(1)
- command = "%s/parsnp %s"%(PARSNP_DIR,inifile.replace(".ini","_mumi.ini"))
+ command = "/usr/lib/parsnp/parsnp %s"%(inifile.replace(".ini","_mumi.ini"))
run_command(command)
try:
mumif = open(outputDir+os.sep+"all.mumi",'r')
@@ -962,14 +948,14 @@ if __name__ == "__main__":
if command == "" and xtrafast and 0:
command = "%s/parsnpA_fast %sparsnpAligner.ini"%(PARSNP_DIR,outputDir+os.sep)
elif command == "":
- command = "%s/parsnp %sparsnpAligner.ini"%(PARSNP_DIR,outputDir+os.sep)
+ command = "/usr/lib/parsnp/parsnp %sparsnpAligner.ini"%(outputDir+os.sep)
else:
- command = "%s/parsnp %spsnn.ini"%(PARSNP_DIR,outputDir+os.sep)
+ command = "/usr/lib/parsnp/parsnp %spsnn.ini"%(outputDir+os.sep)
else:
if not os.path.exists(inifile):
sys.stderr.write("Error: ini file %s does not exist!\n"%(inifile))
sys.exit(1)
- command = "%s/parsnp %s"%(PARSNP_DIR,inifile)
+ command = "/usr/lib/parsnp/parsnp %s"%(inifile)
run_command(command)
@@ -1159,21 +1145,21 @@ if __name__ == "__main__":
if xtrafast or 1:
#add genbank here, if present
if len(genbank_ref) != 0:
- rnc = "%s/harvest -q -o %s/parsnp.ggr -x "%(PARSNP_DIR,outputDir)+outputDir+os.sep+"parsnp.xmfa"
+ rnc = "harvesttools -q -o %s/parsnp.ggr -x "%(outputDir)+outputDir+os.sep+"parsnp.xmfa"
for file in genbank_files:
rnc += " -g %s " %(file)
run_command(rnc)
else:
- run_command("%s/harvest -q -o %s/parsnp.ggr -f %s -x "%(PARSNP_DIR,outputDir,ref)+outputDir+os.sep+"parsnp.xmfa")
+ run_command("harvesttools -q -o %s/parsnp.ggr -f %s -x "%(outputDir,ref)+outputDir+os.sep+"parsnp.xmfa")
if run_recomb_filter:
- run_command("%s/harvest -q -b %s/parsnp.rec,REC,\"PhiPack\" -o %s/parsnp.ggr -i %s/parsnp.ggr"%(PARSNP_DIR,outputDir,outputDir,outputDir))
+ run_command("harvesttools -q -b %s/parsnp.rec,REC,\"PhiPack\" -o %s/parsnp.ggr -i %s/parsnp.ggr"%(outputDir,outputDir,outputDir))
if run_repeat_filter:
- run_command("%s/harvest -q -b %s,REP,\"Intragenomic repeats > 100bp\" -o %s/parsnp.ggr -i %s/parsnp.ggr"%(PARSNP_DIR,repfile,outputDir,outputDir))
+ run_command("harvesttools -q -b %s,REP,\"Intragenomic repeats > 100bp\" -o %s/parsnp.ggr -i %s/parsnp.ggr"%(repfile,outputDir,outputDir))
- run_command("%s/harvest -q -i %s/parsnp.ggr -S "%(PARSNP_DIR,outputDir)+outputDir+os.sep+"parsnp.snps.mblocks")
+ run_command("harvesttools -q -i %s/parsnp.ggr -S "%(outputDir)+outputDir+os.sep+"parsnp.snps.mblocks")
- command = "%s/ft -nt -quote -gamma -slow -boot 100 "%(PARSNP_DIR)+outputDir+os.sep+"parsnp.snps.mblocks > "+outputDir+os.sep+"parsnp.tree"
+ command = "fasttree -nt -quote -gamma -slow -boot 100 "+outputDir+os.sep+"parsnp.snps.mblocks > "+outputDir+os.sep+"parsnp.tree"
print "-->Reconstructing core genome phylogeny.."
run_command(command)
#7)reroot to midpoint
@@ -1204,7 +1190,7 @@ if __name__ == "__main__":
if xtrafast or 1:
#if newick available, add
#new flag to update branch lengths
- run_command("%s/harvest --midpoint-reroot -u -q -i "%(PARSNP_DIR)+outputDir+os.sep+"parsnp.ggr -o "+outputDir+os.sep+"parsnp.ggr -n %s"%(outputDir+os.sep+"parsnp.tree "))
+ run_command("harvesttools --midpoint-reroot -u -q -i "+outputDir+os.sep+"parsnp.ggr -o "+outputDir+os.sep+"parsnp.ggr -n %s"%(outputDir+os.sep+"parsnp.tree "))
print " |->["+OK_GREEN+"OK"+ENDC+"]"
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