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)
programBIN = global_config["Tools"][assembler]["bin"] # in abyss case there is no exectuable
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_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)
programBIN = global_config["Tools"][assembler]["bin"] + "Trinity.pl" # in masurca case there is no exectuable as a make file must be created
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.append("--seqType")
command.append("fq")
command.append("--JM")
command.append("50G")
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.append("--output")
command.append("trinity")
assembler_stdOut = open("trinity.stdOut", "w")
assembler_stdErr = open("trinity.stdErr", "w")
print command
returnValue = subprocess.call(" ".join(command), stdout=assembler_stdOut, stderr=assembler_stdErr, shell=True)
# now align reads back to transcripts
os.chdir("trinity")
programBIN = global_config["Tools"][assembler]["bin"] + "util/alignReads.pl"
command = [programBIN]
command.append("--target")
command.append("Trinity.fasta")
command.append("--seqType")
command.append("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.append("--aligner")
command.append("bowtie")
command.append("--retain_intermediate_files")
print command
returnValue = subprocess.call(" ".join(command), stdout=assembler_stdOut, stderr=assembler_stdErr, shell=True)
# now quantify trnascripts
programBIN = global_config["Tools"][assembler]["bin"] + "util/RSEM_util/run_RSEM_align_n_estimate.pl"
command = [programBIN]
command.append("--transcripts")
command.append("Trinity.fasta")
command.append("--seqType")
command.append("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]))
print 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
