def _prepare_folder_structure(assembler, assemblyDirectory):
if common.directory_exists(assemblyDirectory):
print(
"Assembler {} asumer already computed as folder {} exists".format(
assembler, assemblyDirectory))
return 1
return 0
def _run_abyss_mergePairs(global_config, sample_config,
sorted_libraries_by_insert):
print("running abyss-mergepairs ...")
assembler = "abyss_mergePairs"
outputName = sample_config["output"]
currentDirectory = os.getcwd()
assemblyDirectory = os.path.join(currentDirectory, assembler)
if common.directory_exists(assemblyDirectory):
return sample_config
os.chdir(assemblyDirectory) # now I am in the assembly directory
sorted_libraries_by_insert = common.prepare_folder_structure(
sorted_libraries_by_insert)
# in abyss case there is no exectuable
programBIN = global_config["Tools"][assembler]["bin"]
program_options = global_config["Tools"][assembler]["options"]
if assembler in sample_config:
program_options = sample_config[assembler]
########### HERE IT START THE SPECIFIC ASSEMBLER PART
program = programBIN
command = []
command.append(program)
for option in program_options:
command.append(option)
libraries = {}
for library, libraryInfo in sorted_libraries_by_insert:
read1 = libraryInfo["pair1"]
read2 = libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
insert = libraryInfo["insert"]
std = libraryInfo["std"]
outputNameArray = read1.split('/')[-1].split('_')
outputName = "{}_{}".format(outputNameArray[0], outputNameArray[1])
if orientation == "innie":
if read2 is not None:
currentCommand = command
currentCommand.append('-o')
currentCommand.append(outputName)
currentCommand.append(read1)
currentCommand.append(read2)
abyss_stdOut = open("mergePairs_{}.stdOut".format(outputName),
"a")
abyss_stdErr = open("mergePairs_{}.stdErr".format(outputName),
"a")
print(command)
subprocess.call(command,
stdout=abyss_stdOut,
stderr=abyss_stdErr)
command_mv = [
"mv", "mergePairs_{}.stdErr".format(outputName),
"{}.txt".format(outputName)
]
subprocess.call(command_mv)
os.chdir("..")
return sample_config
def _run_abyss_mergePairs(global_config, sample_config,
sorted_libraries_by_insert):
print("running abyss-mergepairs ...")
assembler = "abyss_mergePairs"
outputName = sample_config["output"]
currentDirectory = os.getcwd()
assemblyDirectory = os.path.join(currentDirectory, assembler)
if common.directory_exists(assemblyDirectory):
return sample_config
os.chdir(assemblyDirectory) # now I am in the assembly directory
sorted_libraries_by_insert = common.prepare_folder_structure(
sorted_libraries_by_insert)
# in abyss case there is no exectuable
programBIN = global_config["Tools"][assembler]["bin"]
program_options = global_config["Tools"][assembler]["options"]
if assembler in sample_config:
program_options=sample_config[assembler]
########### HERE IT START THE SPECIFIC ASSEMBLER PART
program=programBIN
command = []
command.append(program)
for option in program_options:
command.append(option)
libraries = {}
for library, libraryInfo in sorted_libraries_by_insert:
read1 = libraryInfo["pair1"]
read2 = libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
insert = libraryInfo["insert"]
std = libraryInfo["std"]
outputNameArray = read1.split('/')[-1].split('_')
outputName = "{}_{}".format(outputNameArray[0], outputNameArray[1])
if orientation=="innie":
if read2 is not None:
currentCommand = command;
currentCommand.append('-o')
currentCommand.append(outputName)
currentCommand.append(read1)
currentCommand.append(read2)
abyss_stdOut = open("mergePairs_{}.stdOut".format(outputName),
"a")
abyss_stdErr = open("mergePairs_{}.stdErr".format(outputName),
"a")
print(command)
subprocess.call(command, stdout=abyss_stdOut,
stderr=abyss_stdErr)
command_mv = ["mv", "mergePairs_{}.stdErr".format(outputName),
"{}.txt".format(outputName)]
subprocess.call(command_mv)
os.chdir("..")
return sample_config
def _prepare_folder_structure(assembler,assemblyDirectory):
if common.directory_exists(assemblyDirectory):
print("Assembler {} asumer already computed as folder {} exists".format(
assembler,assemblyDirectory))
return 1
return 0
def _run_trinity(global_config, sample_config, sorted_libraries_by_insert):
print("running trinity ...")
assembler = "trinity"
outputName = sample_config["output"]
currentDirectory = os.getcwd()
assemblyDirectory = os.path.join(currentDirectory, assembler)
if common.directory_exists(assemblyDirectory):
return sample_config
os.chdir(assemblyDirectory) # now I am in the assembly directory
sorted_libraries_by_insert = common.prepare_folder_structure(
sorted_libraries_by_insert)
# in masurca case there is no exectuable as a make file must be created
programBIN = global_config["Tools"][assembler]["bin"] + "Trinity"
program_options = global_config["Tools"][assembler]["options"]
if assembler in sample_config:
program_options=sample_config[assembler]
########### HERE IT START THE SPECIFIC ASSEMBLER PART
command = [programBIN]
command.extend(["--seqType", "fq"])
command.extend(["--JM", "100G"])
if "threads" in sample_config:
command.extend(["--CPU", str(sample_config["threads"])])
for library, libraryInfo in sorted_libraries_by_insert:
read1 = libraryInfo["pair1"]
read2 = libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
insert = libraryInfo["insert"]
std = libraryInfo["std"]
if read2 is None:
command.append("--single")
command.append("{}".format(read1))
elif orientation=="innie":
command.append("--left")
command.append("{}".format(read1))
command.append("--right")
command.append("{}".format(read2))
else:
print("trinity: somthing wrong or unexpected in the sample",
"config file")
return sample_config
command.extend(["--output", "trinity"])
assembler_stdOut = open("trinity.stdOut", "w")
assembler_stdErr = open("trinity.stdErr", "w")
print(" ".join(command))
returnValue = subprocess.call(" ".join(command), stdout=assembler_stdOut,
stderr=assembler_stdErr, shell=True)
# now align reads back to transcripts and estimate abundance
os.chdir("trinity")
programBIN = global_config["Tools"][assembler]["bin"] + \
"util/align_and_estimate_abundance.pl"
command = [programBIN]
command.extend(["--transcripts", "Trinity.fasta"])
command.extend(["--seqType", "fq"])
for library, libraryInfo in sorted_libraries_by_insert:
read1 = libraryInfo["pair1"]
read2 = libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
insert = libraryInfo["insert"]
std = libraryInfo["std"]
if read2 is not None and orientation == "innie":
command.append("--left")
command.append("{}".format(os.path.splitext(read1)[0]))
command.append("--right")
command.append("{}".format(os.path.splitext(read2)[0]))
command.extend(["--aln_method", "bowtie"])
command.extend(["--est_method", "RSEM"])
command.append("--debug")
command.append("--trinity_mode")
command.append("--prep_reference")
if "threads" in sample_config:
command.extend(["--thread_count", str(sample_config["threads"])])
print(" ".join(command))
returnValue = subprocess.call(" ".join(command), stdout=assembler_stdOut,
stderr=assembler_stdErr, shell=True)
#now copy results
os.chdir("..")
subprocess.call(["cp", "trinity/Trinity.fasta",
"{}.fasta".format(outputName)])
subprocess.call(["cp", "trinity/RSEM.isoforms.results",
"{}.isoforms.results".format(outputName)])
subprocess.call(["cp", "trinity/RSEM.genes.results",
"{}.genes.results".format(outputName)])
os.chdir(currentDirectory)
return sample_config
def _run_trinity(global_config, sample_config, sorted_libraries_by_insert):
print("running trinity ...")
assembler = "trinity"
outputName = sample_config["output"]
currentDirectory = os.getcwd()
assemblyDirectory = os.path.join(currentDirectory, assembler)
if common.directory_exists(assemblyDirectory):
return sample_config
os.chdir(assemblyDirectory) # now I am in the assembly directory
sorted_libraries_by_insert = common.prepare_folder_structure(
sorted_libraries_by_insert)
# in masurca case there is no exectuable as a make file must be created
programBIN = global_config["Tools"][assembler]["bin"] + "Trinity"
program_options = global_config["Tools"][assembler]["options"]
if assembler in sample_config:
program_options = sample_config[assembler]
########### HERE IT START THE SPECIFIC ASSEMBLER PART
command = [programBIN]
command.extend(["--seqType", "fq"])
command.extend(["--JM", "100G"])
if "threads" in sample_config:
command.extend(["--CPU", str(sample_config["threads"])])
for library, libraryInfo in sorted_libraries_by_insert:
read1 = libraryInfo["pair1"]
read2 = libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
insert = libraryInfo["insert"]
std = libraryInfo["std"]
if read2 is None:
command.append("--single")
command.append("{}".format(read1))
elif orientation == "innie":
command.append("--left")
command.append("{}".format(read1))
command.append("--right")
command.append("{}".format(read2))
else:
print("trinity: somthing wrong or unexpected in the sample",
"config file")
return sample_config
command.extend(["--output", "trinity"])
assembler_stdOut = open("trinity.stdOut", "w")
assembler_stdErr = open("trinity.stdErr", "w")
print(" ".join(command))
returnValue = subprocess.call(" ".join(command),
stdout=assembler_stdOut,
stderr=assembler_stdErr,
shell=True)
# now align reads back to transcripts and estimate abundance
os.chdir("trinity")
programBIN = global_config["Tools"][assembler]["bin"] + \
"util/align_and_estimate_abundance.pl"
command = [programBIN]
command.extend(["--transcripts", "Trinity.fasta"])
command.extend(["--seqType", "fq"])
for library, libraryInfo in sorted_libraries_by_insert:
read1 = libraryInfo["pair1"]
read2 = libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
insert = libraryInfo["insert"]
std = libraryInfo["std"]
if read2 is not None and orientation == "innie":
command.append("--left")
command.append("{}".format(os.path.splitext(read1)[0]))
command.append("--right")
command.append("{}".format(os.path.splitext(read2)[0]))
command.extend(["--aln_method", "bowtie"])
command.extend(["--est_method", "RSEM"])
command.append("--debug")
command.append("--trinity_mode")
command.append("--prep_reference")
if "threads" in sample_config:
command.extend(["--thread_count", str(sample_config["threads"])])
print(" ".join(command))
returnValue = subprocess.call(" ".join(command),
stdout=assembler_stdOut,
stderr=assembler_stdErr,
shell=True)
#now copy results
os.chdir("..")
subprocess.call(
["cp", "trinity/Trinity.fasta", "{}.fasta".format(outputName)])
subprocess.call([
"cp", "trinity/RSEM.isoforms.results",
"{}.isoforms.results".format(outputName)
])
subprocess.call([
"cp", "trinity/RSEM.genes.results",
"{}.genes.results".format(outputName)
])
os.chdir(currentDirectory)
return sample_config