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ABySS, SOAPdenovo, SPADES fully supported
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Francesco Vezzi committed Oct 31, 2013
1 parent fca2d15 commit 0c7cab7
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Showing 2 changed files with 93 additions and 51 deletions.
2 changes: 1 addition & 1 deletion config_de_novo.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ assemble:
bin: /home/vezzi/assembly_pipeline/tools/SPAdes-2.5.1-Linux/bin/spades.py
options: ["--careful", "-t 8"]
cabog:
bin:
bin: /home/vezzi/assembly_pipeline/tools/wgs-7.0/Linux-amd64/bin/
options: [""]
allpaths:
bin: TODO
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142 changes: 92 additions & 50 deletions script/assemble.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,30 +37,33 @@ def _run_soapdenovo(global_config, sample_config, sorted_libraries_by_insert):
print "done (soapdenovo folder already present, assumed already run)"
return
os.chdir(soapFolder)
programBIN = global_config["assemble"]["soapdenovo"]["bin"] # in masurca case there is no exectuable as a make file must be created
program_options=global_config["assemble"]["soapdenovo"]["options"]
programBIN = global_config["assemble"]["soapdenovo"]["bin"] # in masurca case there is no exectuable as a make file must be created
program_options =global_config["assemble"]["soapdenovo"]["options"]
kmer = sample_config["kmer"]

soap_config_file = open("configuration.txt", "w")
soap_config_file.write("max_rd_len=250\n") #TODO make this a parameter in the options
rank = 1
for library, libraryInfo in sorted_libraries_by_insert:
soap_config_file.write("[LIB]\n")
read1=libraryInfo["pair1"]
read2=libraryInfo["pair2"]
read1 =libraryInfo["pair1"]
read2 =libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
insert = libraryInfo["insert"]
std = libraryInfo["std"]
soap_config_file.write("avg_ins={}\n".format(insert))
soap_config_file.write("rank={}\n".format(rank))
rank += 1
soap_config_file.write("map_len=30\n")

if orientation=="innie":
if orientation=="innie" or orientation=="none":
soap_config_file.write("asm_flags=3\n")
soap_config_file.write("pair_num_cutoff=3\n")
soap_config_file.write("reverse_seq=0\n")
soap_config_file.write("q1={}\n".format(read1))
soap_config_file.write("q2={}\n".format(read2))
if read2 is None:
soap_config_file.write("q={}\n".format(read1))
else:
soap_config_file.write("q1={}\n".format(read1))
soap_config_file.write("q2={}\n".format(read2))
elif orientation=="outtie":
soap_config_file.write("asm_flags=2\n")
soap_config_file.write("pair_num_cutoff=5\n")
Expand All @@ -69,20 +72,24 @@ def _run_soapdenovo(global_config, sample_config, sorted_libraries_by_insert):
soap_config_file.write("q2={}\n".format(read2))

soap_config_file.close()

masurca_stdOut = open("soap.stdOut", "w")
masurca_stdErr = open("soap.stdErr", "w")
command = [programBIN , "all", "-s", "configuration.txt", "-K", "53", "-o", "soapAssembly", "-p" , "8" ] # TODO: make everyhitn more parameter dependent
subprocess.call(command, stdout=masurca_stdOut, stderr=masurca_stdErr)


if(os.path.exists("soapAssembly.scafSeq")):
os.rename("soapAssembly.scafSeq", "{}.fasta".format(outputName))
soap_stdOut = open("soap.stdOut", "w")
soap_stdErr = open("soap.stdErr", "w")
os.makedirs(os.path.join(soapFolder, "runSOAP"))
os.chdir("runSOAP")
command = [programBIN , "all", "-s", "../configuration.txt", "-K", "{}".format(kmer), "-o", "soapAssembly", "-p" , "8" ] # TODO: make everyhitn more parameter dependent
returnValue = subprocess.call(command, stdout=soap_stdOut, stderr=soap_stdErr)
os.chdir("..")
if returnValue == 0:
if(os.path.exists(os.path.join("runSOAP","soapAssembly.scafSeq"))):
subprocess.call(["mv", os.path.join("runSOAP","soapAssembly.scafSeq"), "{}.scf.fasta".format(outputName) ])
subprocess.call(["mv", os.path.join("runSOAP","soapAssembly.contig"), "{}.ctg.fasta".format(outputName) ])
subprocess.call(["rm", "-r", "runSOAP"])
else:
print "something wrong with SOAPdenovo -> no contig file generated"
else:
print "something wrong with soapdenovo!!!"

print "SOAPdenovo terminated with an error. Please check running folder for more informations"
os.chdir("..")
print "soap succesfully exectued"
print "SOAPdenovo exectued"
return


Expand Down Expand Up @@ -114,17 +121,18 @@ def _run_masurca(global_config, sample_config, sorted_libraries_by_insert):
libraryPEnum = 0
libraryMP = "m"
libraryMPnum = 0

#TODO: single ended reads
for library, libraryInfo in sorted_libraries_by_insert:
read1=libraryInfo["pair1"]
read2=libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
insert = libraryInfo["insert"]
std = libraryInfo["std"]
if orientation=="innie":
configurationLine = "PE = {}{} {} {} {} {}".format(libraryPE, allTheLetters[libraryPEnum], insert, std, read1, read2)
masurca_config_file.write("{}\n".format(configurationLine))
libraryPEnum+=1 #TODO: check when more than 21 PE libraries ae specified
if read2 is not None:
configurationLine = "PE = {}{} {} {} {} {}".format(libraryPE, allTheLetters[libraryPEnum], insert, std, read1, read2)
masurca_config_file.write("{}\n".format(configurationLine))
libraryPEnum+=1 #TODO: check when more than 21 PE libraries ae specified
elif orientation=="outtie":
configurationLine = "JUMP = {}{} {} {} {} {}".format(libraryMP, allTheLetters[libraryMPnum], insert, std, read1, read2)
masurca_config_file.write("{}\n".format(configurationLine))
Expand Down Expand Up @@ -160,19 +168,32 @@ def _run_masurca(global_config, sample_config, sorted_libraries_by_insert):
command = [os.path.join(programPATH,"bin/runSRCA.pl") , "configuration.txt"]
subprocess.call(command, stdout=masurca_stdOut, stderr=masurca_stdErr)

if(os.path.exists("assemble.sh")):
command = ["assemble.sh"]
subprocess.call(command, stdout=masurca_stdOut, stderr=masurca_stdErr)

if not os.path.exists("assemble.sh"):
print "MaSuRCA: assemble.sh not created. Unknown failure"
return
command = ["./assemble.sh"]
returnValue = subprocess.call(command, stdout=masurca_stdOut, stderr=masurca_stdErr)
if returnValue == 0:
#if os.path.exists(os.path.join("runABySS","{}-contigs.fa".format(outputName))):
# subprocess.call(["cp", os.path.join("runABySS","{}-contigs.fa".format(outputName)), "{}.ctg.fasta".format(outputName) ])
# subprocess.call(["cp", os.path.join("runABySS","{}-scaffolds.fa".format(outputName)), "{}.scaf.fasta".format(outputName) ])
# subprocess.call(["rm", "-r", "runABySS"])
#else:
# print "something wrong with MaSuRCA -> no contig file generated"
else:
print "MaSuRCA terminated with an error. Please check running folder for more informations"
os.chdir("..")
print "masurca succesfully exectued"
print "MaSuRCA executed"
return





def _run_abyss(global_config, sample_config, sorted_libraries_by_insert):
print "running abyss ..."
##TO DO ::: avoid to load module
##subprocess.call(["module","load","abyss/1.3.5"])
outputName = sample_config["output"]
mainDir = os.getcwd()
abyssFolder = os.path.join(os.getcwd(), "abyss")
Expand Down Expand Up @@ -201,7 +222,7 @@ def _run_abyss(global_config, sample_config, sorted_libraries_by_insert):
orientation = libraryInfo["orientation"]
insert = libraryInfo["insert"]
std = libraryInfo["std"]
if orientation=="innie":
if orientation=="innie" or orientation=="none":
if read2 is None:
if "se" not in libraries: # check if this is the first time I insert a se file
libraries["se"] = "se=\'"
Expand All @@ -220,14 +241,11 @@ def _run_abyss(global_config, sample_config, sorted_libraries_by_insert):
if not libName in libraries["mp"]:
libraries["mp"][libName] = ""
libraries["mp"][libName] += libraries["mp"][libName] + "{} {} ".format(read1, read2)
#now creat the command

#now create the command
command += "name={} ".format(outputName)

librariesSE = ""
librariesPE = ""
librariesMP = ""

if "se" in libraries:
libraries["se"] = libraries["se"] + "\'"
librariesSE = libraries["se"]
Expand All @@ -250,9 +268,21 @@ def _run_abyss(global_config, sample_config, sorted_libraries_by_insert):
command += "{} ".format(librariesPE)
command += "{} ".format(librariesMP)

subprocess.call(command, stdout=abyss_stdOut, stderr=abyss_stdErr, shell=True)
os.makedirs(os.path.join(abyssFolder, "runABySS"))
os.chdir("runABySS")
returnValue = subprocess.call(command, stdout=abyss_stdOut, stderr=abyss_stdErr, shell=True)
os.chdir("..")

if returnValue == 0:
if os.path.exists(os.path.join("runABySS","{}-contigs.fa".format(outputName))):
subprocess.call(["cp", os.path.join("runABySS","{}-contigs.fa".format(outputName)), "{}.ctg.fasta".format(outputName) ])
subprocess.call(["cp", os.path.join("runABySS","{}-scaffolds.fa".format(outputName)), "{}.scaf.fasta".format(outputName) ])
subprocess.call(["rm", "-r", "runABySS"])
else:
print "something wrong with ABySS -> no contig file generated"
else:
print "ABySS terminated with an error. Please check running folder for more informations"
os.chdir("..")
print "abyss executed"
return


Expand Down Expand Up @@ -359,17 +389,18 @@ def _run_spades(global_config, sample_config, sorted_libraries_by_insert):

command += "-o {} ".format(outputName)

print command
subprocess.call(command, stdout=spades_stdOut, stderr=spades_stdErr, shell=True)
command = ["mv", "{}/contigs.fasta".format(outputName), "{}_contigs.fasta".format(outputName)]
subprocess.call(command, stdout=spades_stdOut, stderr=spades_stdErr)
command = ["mv", "{}/scaffolds.fasta".format(outputName), "{}_scaffolds.fasta".format(outputName)]
subprocess.call(command, stdout=spades_stdOut, stderr=spades_stdErr)
command = ["rm", "-r", outputName]
subprocess.call(command, stdout=spades_stdOut, stderr=spades_stdErr)
returnValue = subprocess.call(command, stdout=spades_stdOut, stderr=spades_stdErr, shell=True)
if returnValue == 0:
if os.path.exists(os.path.join("outputName","contigs.fasta")):
subprocess.call(["cp", os.path.join("outputName","contigs.fasta"), "{}.ctg.fasta".format(outputName)])
subprocess.call(["cp", os.path.join("outputName","scaffoldss.fasta"), "{}.scf.fasta".format(outputName)])
subprocess.call(["rm", "-r", outputName])
else:
print "something wrong with SPADES -> no contig file generated"
else:
print "SPADES terminated with an error. Please check running folder for more informations"

os.chdir("..")

return


Expand All @@ -393,7 +424,7 @@ def _run_cabog(global_config, sample_config, sorted_libraries_by_insert):
cabog_stdOut = open("cabog.stdOut", "w")
cabog_stdErr = open("cabog.stdErr", "w")
for library, libraryInfo in sorted_libraries_by_insert:
command_fastqToCA = "fastqToCA "
command_fastqToCA = os.path.join(programBIN, "fastqToCA")
read1=libraryInfo["pair1"]
read2=libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
Expand Down Expand Up @@ -422,14 +453,25 @@ def _run_cabog(global_config, sample_config, sorted_libraries_by_insert):
command_fastqToCA += " {},{} ".format(read1, read2)
command_fastqToCA += " > "
command_fastqToCA += " {}_{}.frg ".format(outputName, libraries)
print command_fastqToCA
subprocess.call(command_fastqToCA, stderr=cabog_stdErr, shell=True)
libraries += 1

command_runCA = "runCA -d . -p {} *frg".format(outputName)
subprocess.call(command_runCA, stdout=cabog_stdOut, stderr=cabog_stdErr, shell=True)
command_runCA = os.path.join(programBIN, "runCA")
command_runCA += " -d runCABOGfolder -p {} *frg".format(outputName)
returnValue = subprocess.call(command_runCA, stdout=cabog_stdOut, stderr=cabog_stdErr, shell=True)
if returnValue == 0:
#assembly succed, remove files and save assembly
if os.path.exists(os.path.join("runCABOGfolder","9-terminator", "{}.ctg.fasta".format(outputName))):
subprocess.call(["mv", os.path.join("runCABOGfolder","9-terminator", "{}.ctg.fasta".format(outputName)), "{}.ctg.fasta".format(outputName)])
subprocess.call(["mv", os.path.join("runCABOGfolder","9-terminator", "{}.scf.fasta".format(outputName)), "{}.scf.fasta".format(outputName)])
subprocess.call(["rm", "-r", "runCABOGfolder"])
else:
print "something wrong with CABOG -> no contig file generated"
else:
print "CABOG terminated with an error. Please check running folder for more informations"

os.chdir("..")
print "CABOG succesfully exectued"
print "CABOG exectued"
return


Expand Down

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