def runMikado(self,
sub_command,
valid_args=None,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper to run mikado
"""
valid_commands = [
'configure', 'prepare', 'serialise', 'pick', 'compare'
]
if sub_command not in valid_commands:
pu.print_boldred("Invalid command: " + sub_command +
". Exiting...")
return False
mikado_Cmd = ['mikado', sub_command]
#add options
mikado_Cmd.extend(pu.parse_unix_args(valid_args, kwargs))
#print("Executing:"+" ".join(mergedArgsDict))
#start ececution
status = pe.execute_command(mikado_Cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("mikado failed")
#return status
return status
def test_linux_args():
res = ['-O', './test', 'IN1', 'IN2']
assert pu.parse_unix_args(['-O', '-t', '-q'], {
"-O": "./test",
"Attr2": "XX",
"--": ("IN1", "IN2")
}) == res, 'linux args failed'
def run_trinity(self,valid_args_list=None,verbose=False,quiet=False,logs=True,objectid="NA",**kwargs):
"""Wrapper for running trinity
Parameters
----------
valid_args: list
list of valid arguments
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession.
kwargs: dict
Options passed to trinity
:return: Return the status of trinity command.
:rtype: bool
"""
trinity_cmd=['Trinity']
#add options
trinity_cmd.extend(pu.parse_unix_args(valid_args_list,kwargs))
#start ececution
status=pe.execute_command(trinity_cmd,verbose=verbose,quiet=quiet,logs=logs,objectid=objectid)
if not status:
pu.print_boldred("trinity failed")
#return status
return status
def run_star(self,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running star.
The self.star_index index used.
Parameters
----------
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
Options to pass to stringtie. This will override the existing options in self.passed_args_dict (only replace existing arguments and not replace all the arguments).
kwargs: dict
arguments to pass to star. This will override parametrs already existing in the self.passedArgumentList list but NOT replace all of them.
:return: Returns the status of star. True is passed, False if failed.
:rtype: bool
"""
#check for a valid index
if not self.check_index():
raise Exception(
"ERROR: Invalid star index. Please run build index to generate an index."
)
#override existing arguments
mergedArgsDict = {**self.passedArgumentDict, **kwargs}
star_cmd = ['STAR']
#add options
star_cmd.extend(pu.parse_unix_args(self.valid_args, mergedArgsDict))
#execute command
cmd_status = pe.execute_command(star_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not cmd_status:
print("STAR failed:" + " ".join(star_cmd))
#return status
return cmd_status
def run_cuff(self,
command,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running cuff* commands
Parameters
----------
command: string
the command name
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession.
kwargs: dict
Options passed to command
:return: Returns the status of the command.
:rtype: bool
"""
validCommands = [
'cuffcompare', 'cuffdiff', 'cufflinks', 'cuffmerge', 'cuffnorm',
'cuffquant'
]
if command in validCommands:
#override existing arguments
merged_args_dict = {**self.passed_args_dict, **kwargs}
cuff_cmd = [command]
#add options
cuff_cmd.extend(
pu.parse_unix_args(self.valid_args_list, merged_args_dict))
#start ececution
status = pe.execute_command(cuff_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("cufflinks failed")
#return status
return status
else:
pu.print_boldred("Unknown command {}" + command)
return False
def run_hisat2(self,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running hisat2.
Run HISAT2 using and SRA object and produce .bam file as result. The HISAT2 index used will be self.hisat2_index.
All output will be written to SRA.location by default.
Parameters
----------
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
arg: dict
arguments to pass to hisat2. This will override parametrs already existing in the self.passedArgumentList list but NOT replace them.
:return: Returns the status of hisat2. True is passed, False if failed.
:rtype: bool
"""
#check for a valid index
if not self.check_index():
raise Exception(
"ERROR: Invalid HISAT2 index. Please run build index to generate an index."
)
#override existing arguments
mergedArgsDict = {**self.passedArgumentDict, **kwargs}
hisat2_Cmd = ['hisat2']
#add options
hisat2_Cmd.extend(pu.parse_unix_args(self.valid_args, mergedArgsDict))
#execute command
cmd_status = pe.execute_command(hisat2_Cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not cmd_status:
print("hisat2 failed:" + " ".join(hisat2_Cmd))
#return status
return cmd_status
def run_salmon(self,
subcommand,
valid_args=None,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running salmon.
Parameters
----------
subcommand: str
subcommand for salmon
valid_args: list
List of valid arguments
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
Options to pass to salmon. This will override the existing options
:return: Returns the status of salmon. True is passed, False if failed.
:rtype: bool
"""
#check for a valid index
if subcommand != "index":
if not self.check_index():
raise Exception(
"ERROR: Invalid salmon index. Please run build index to generate an index."
)
salmon_Cmd = ['salmon', subcommand]
salmon_Cmd.extend(pu.parse_unix_args(valid_args, kwargs))
#start ececution
status = pe.execute_command(salmon_Cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid,
command_name=" ".join(salmon_Cmd[0:2]))
if not status:
pu.print_boldred("salmon failed")
return status
def run_portcullis(self,
sub_command,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""
Wrapper to run portcullis.
Parameters
----------
sub_command: string
sub_command to pass to portcullis e.g. full, prep, junc etc.
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
arguments to pass to portcullis. This will override parametrs already existing in the self.passedArgumentDict list but NOT replace them.
:return: Returns the status of portcullis. True is passed, False if failed.
:rtype: bool
"""
#override existing arguments
mergedArgsDict = {**self.passedArgumentDict, **kwargs}
portcullis_cmd = ['portcullis', sub_command]
#add options
portcullis_cmd.extend(
pu.parse_unix_args(self.valid_args, mergedArgsDict))
print("Executing:" + " ".join(portcullis_cmd))
#start ececution
status = pe.execute_command(portcullis_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("portcullis failed")
#return status
return status
def run_diamond(self,
subcommand,
valid_args=None,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running diamond.
Parameters
----------
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
arguments to pass to hisat2. This will override parametrs already existing in the self.passedArgumentList list but NOT replace them.
:return: Returns the status of diamond. True is passed, False if failed.
:rtype: bool
"""
#check for a valid index
if subcommand == "blastx" or subcommand == "blastp":
if not self.check_index():
raise Exception(
"ERROR: Invalid Diamond index. Please run build_index() to generate an index."
)
diamond_cmd = ['diamond', subcommand]
#add options
diamond_cmd.extend(pu.parse_unix_args(valid_args, kwargs))
#execute command
cmd_status = pe.execute_command(diamond_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not cmd_status:
print("Diamond failed:" + " ".join(diamond_cmd))
#return status
return cmd_status
def run_hisat2(self,
valid_args=None,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running hisat2.
Parameters
----------
valid_args: list
list of valid arguments
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
arguments to pass to hisat2.
:return: Returns the status of hisat2. True is passed, False if failed.
:rtype: bool
"""
#check for a valid index
if not self.check_index():
raise Exception(
"ERROR: Invalid HISAT2 index. Please run build index to generate an index."
)
hisat2_Cmd = ['hisat2']
#add options
hisat2_Cmd.extend(pu.parse_unix_args(valid_args, kwargs))
#execute command
cmd_status = pe.execute_command(hisat2_Cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not cmd_status:
print("hisat2 failed:" + " ".join(hisat2_Cmd))
#return status
return cmd_status
def run_bowtie2(self,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running bowtie2.
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
arguments to pass to bowtie2. This will override parametrs already existing in the self.passedArgumentList list but NOT replace them.
:return: Returns the status of bowtie2. True is passed, False if failed.
:rtype: bool
"""
#check for a valid index
if not self.check_index():
raise Exception(
"ERROR: Invalid Bowtie2 index. Please run build index to generate an index."
)
#override existing arguments
mergedArgsDict = {**self.passedArgumentDict, **kwargs}
bowtie2_cmd = ['bowtie2']
bowtie2_cmd.extend(pu.parse_unix_args(self.valid_args, mergedArgsDict))
#print("Executing:"+" ".join(bowtie2_cmd))
#start ececution
status = pe.execute_command(bowtie2_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("bowtie2 failed")
return status
def run_samtools(self,
sub_command,
valid_args=None,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""A wrapper to run samtools.
Parameters
----------
sub_command: string
sub_command to pass to samtools e.g. sort, merge etc
valid_args: list
A list containing valid parameters. Parameters in kwargs not in this list will be ignored. Default: None
arg1: dict
arguments to pass to samtools.
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
Options to pass to samtools. This will override the existing options
:return: Returns the status of samtools. True is passed, False if failed.
:rtype: bool
"""
samtools_cmd = ['samtools', sub_command]
#add options
samtools_cmd.extend(pu.parse_unix_args(valid_args, kwargs))
#start ececution
status = pe.execute_command(samtools_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("samtools failed")
#return status
return status
def run_portcullis(self,
sub_command,
valid_args=None,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""
Wrapper to run portcullis.
Parameters
----------
sub_command: string
sub_command to pass to portcullis e.g. full, prep, junc etc.
valid_args: list
A list of valid arguments. Arguments outside this list will be ignored. If empty or None, accepts all arguments.
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
arguments to pass to portcullis.
:return: Returns the status of portcullis. True is passed, False if failed.
:rtype: bool
"""
portcullis_cmd = ['portcullis', sub_command]
#add options
portcullis_cmd.extend(pu.parse_unix_args(valid_args, kwargs))
#start ececution
status = pe.execute_command(portcullis_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("portcullis failed")
#return status
return status
def run_stringtie(self,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running stringtie. This can be used to run stringtie without using perform_assembly() function.
Parameters
----------
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
Options to pass to stringtie. This will override the existing options in self.passed_args_dict (only replace existing arguments and not replace all the arguments).
:return: Returns the status of stringtie command.
:rtype: bool
"""
#override existing arguments
merged_args_dict = {**self.passed_args_dict, **kwargs}
stie_cmd = ['stringtie']
#add options
stie_cmd.extend(
pu.parse_unix_args(self.valid_args_list, merged_args_dict))
#start ececution
status = pe.execute_command(stie_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("stringtie failed")
#return status
return status
def run_trimgalore(self,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running trimgalore
Parameters
----------
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
Options to pass to trimgalore (will override existing parameters)
:return: Status of trimgalore command
:rtype: bool
"""
#override existing arguments
mergedArgsDict = {**self.passedArgumentDict, **kwargs}
#create command to run
trimgalore_cmd = ['trim_galore']
trimgalore_cmd.extend(
pu.parse_unix_args(self.valid_args, mergedArgsDict))
#start ececution
status = pe.execute_command(trimgalore_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("trimgalore failed")
#return status
return status
def run_cufflinks(self,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running cufflinks
Parameters
----------
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession.
kwargs: dict
Options passed to cufflinks
:return: Returns the status of cufflinks command.
:rtype: bool
"""
#override existing arguments
merged_args_dict = {**self.passed_args_dict, **kwargs}
cufflinks_cmd = ['cufflinks']
#add options
cufflinks_cmd.extend(
pu.parse_unix_args(self.valid_args_list, merged_args_dict))
#start ececution
status = pe.execute_command(cufflinks_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("cufflinks failed")
#return status
return status
def run_transdecoder(self,
command,
valid_args=None,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Wrapper for running transdecoder.
Parameters
----------
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
arguments to pass to hisat2. This will override parametrs already existing in the self.passedArgumentList list but NOT replace them.
:return: Returns the status of diamond. True is passed, False if failed.
:rtype: bool
"""
txd_cmd = [command]
#add options
txd_cmd.extend(pu.parse_unix_args(valid_args, kwargs))
#execute command
cmd_status = pe.execute_command(txd_cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not cmd_status:
print("Transdecoder failed:" + " ".join(txd_cmd))
#return status
return cmd_status
def runRibocode(self,
gtf,
genome,
bam,
l="no",
outsuffix="ribocode_out",
verbose=False,
quiet=False,
logs=True,
objectid="NA"):
"""Wrapper to run ribocode in one step
"""
#check input
if not pu.check_files_exist(gtf, genome, bam):
pu.print_boldred("Please check input files for Ribocode")
return ""
out_dir = pu.get_file_directory(gtf)
outFile = os.path.join(out_dir, outsuffix)
newOpts = {"-g": gtf, "f": genome, "-r": bam, "-l": l, "-o": outFile}
ribocode_Cmd = ['RiboCode_onestep']
ribocode_Cmd.extend(pu.parse_unix_args(self.valid_args, newOpts))
status = pe.execute_command(ribocode_Cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("ribocode failed")
return ""
return outFile
def build_index(self,
index_path,
index_name,
*args,
threads=None,
overwrite=False,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Build a hisat index with given parameters and saves the new index to self.hisat2_index.
Parameters
----------
index_path: string
Path where the index will be created
index_name: string
A name for the index
args: tuple
Path to reference input files
threads: int
Num threads to use
verbose : bool
Print stdout and std error
quiet : bool
Print nothing
logs : bool
Log this command to pyrpipe logs
objectid : string
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
Parameters for the hisat2-build command
:return: Returns the status of hisat2-build
:rtype: bool
"""
#check input references
if len(args) < 1:
pu.print_boldred(
"No reference sequence provided to hisat2-build. Exiting")
return False
if not pu.check_files_exist(*args):
pu.print_boldred(
"Please check input reference sequences provided to hisat2-build. Exiting"
)
return False
print("Building hisat index...")
hisat2Buildvalid_args = [
'-c', '--large-index', '-a', '-p', '--bmax', '--bmaxdivn', '--dcv',
'--nodc', '-r', '-3', '-o', '-t', '--localoffrate',
'--localftabchars', '--snp', '--haplotype', '--ss', '--exon',
'--seed', '-q', '-h', '--usage', '--version'
]
#create the out dir
if not pu.check_paths_exist(index_path):
if not pu.mkdir(index_path):
print(
"ERROR in building hisat2 index. Failed to create index directory."
)
return False
if not overwrite:
#check if files exists
if pu.check_hisatindex(os.path.join(index_path, index_name)):
print("Hisat2 index with same name already exists. Exiting...")
self.hisat2_index = os.path.join(index_path, index_name)
return True
#handle threads
if not threads:
threads = self.threads
hisat2Build_Cmd = ['hisat2-build']
newOpts = {"-p": str(threads)}
mergedOpts = {**newOpts, **kwargs}
#add options
hisat2Build_Cmd.extend(
pu.parse_unix_args(hisat2Buildvalid_args, mergedOpts))
#add input files
hisat2Build_Cmd.append(str(",".join(args)))
#add dir/basenae
hisat2Build_Cmd.append(os.path.join(index_path, index_name))
#print("Executing:"+str(" ".join(hisat2Build_Cmd)))
#start ececution
status = pe.execute_command(hisat2Build_Cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("hisatBuild failed")
return False
#check index files
if not pu.check_hisatindex(os.path.join(index_path, index_name)):
pu.print_boldred("hisatBuild failed")
return False
#set the index path
self.hisat2_index = os.path.join(index_path, index_name)
#return status
return True
def run_fasterqdump(self,
delete_sra=False,
verbose=False,
quiet=False,
logs=True,
**kwargs):
"""Execute fasterq-dump to convert .sra file to fastq files.
The fastq files will be stored in the same directory as the sra file. All fastq files should be consistently named
using the extension .fastq
Parameters
----------
delete_sra: bool
delete sra file after completion
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
kwargs: dict
A dict containing fasterq-dump arguments
:return: Return status of the fasterq-dump command. True if successful download and False if failed.
:rtype: bool
Examples
--------
>>> object.run_fasterqdump()
True
"""
#check if fastq files exists already
if self.fastqFilesExistsLocally():
pu.print_green("Fastq files exist already")
return True
#first check is sra exists
if not self.sraFileExistsLocally():
pu.print_boldred(
"Error executing fasterq-dump: .sra file not found. Please run download_sra()."
)
return False
#else directly run fasterq-dump on accession ?
fasterqdumpArgsList = [
'-f', '-t', '-s', '-N', '-X', '-a', '-p', '-c', '-o', '-O', '-h',
'-V', '-L', '-v', '-q', '-b', '-m', '-e', '-x', '-S', '-3', '-P',
'-M', '-B', '--option-file', '--strict', '--table',
'--include-technical', '--skip-technical', '--concatenate-reads'
]
#ignore location and file name arguments if given
if '-O' in kwargs:
print("Ignoring -O flag." + " location is: " + self.location)
#delete -O parameter
del kwargs['-O']
if '-o' in kwargs:
print("Ignoring -o flag." + " File name is: " + self.srr_accession)
#delete -o parameter
del kwargs['-o']
#execute command
fstrqd_Cmd = ['fasterq-dump']
fstrqd_Cmd.extend(pu.parse_unix_args(fasterqdumpArgsList, kwargs))
#add location
fstrqd_Cmd.extend(['-O', self.location])
#add output filename. output will be <srr_accession>.fastq or <srr_accession>_1.fastq and <srr_accession>_2.fastq
fstrqd_Cmd.extend(['-o', self.srr_accession + ".fastq"])
fstrqd_Cmd.append(self.localSRAFilePath)
#execute command
cmdStatus = pe.execute_command(fstrqd_Cmd, objectid=self.srr_accession)
if not cmdStatus:
print("fasterqdump failed for:" + self.srr_accession)
return False
#check if fastq files are downloaded
if (self.layout == "SINGLE"):
self.localfastqPath = os.path.join(self.location,
self.srr_accession + ".fastq")
if not pu.check_files_exist(self.localfastqPath):
pu.print_boldred("Error running fasterq-dump file. File " +
self.localfastqPath + " does not exist!!!")
return False
else:
self.localfastq1Path = os.path.join(
self.location, self.srr_accession + "_1.fastq")
self.localfastq2Path = os.path.join(
self.location, self.srr_accession + "_2.fastq")
if not pu.check_files_exist(self.localfastq1Path,
self.localfastq2Path):
pu.print_boldred("Error running fasterq-dump file. File " +
self.localfastq1Path + " does not exist!!!")
return False
#delete sra file if specified
if delete_sra:
self.delete_sra()
return True
def download_sra(self, verbose=False, quiet=False, logs=True, **kwargs):
"""This function downloads .sra file from NCBI SRA servers using the prefetch command.
NCBI sra-toolkit 2.9 or higher must be installed on the system in order to use prefetch.
prefetch will create a folder with name same as <srr_accession> under the location (path) specified.
The path of downloaded file is saved in the object as localSRAPath. This localSRAPath is then used
by other functions to access the downloaded data.
The **kwargs is for passing arguments to the prefetch command.
Parameters
----------
kwargs: dict
dict containing additional prefetch arguments
:return: Return status of the prefetch command. True if successful download and False if failed.
:rtype: bool
Examples
--------
>>> object.download_sra()
True
"""
#store path to the downloaded sra file
self.localSRAFilePath = os.path.join(self.location,
self.srr_accession + ".sra")
#check if already exists
if pu.check_files_exist(self.localSRAFilePath):
pu.print_green("File already exists:" + self.localSRAFilePath)
#save file .sra file size
self.sraFileSize = pu.get_file_size(self.localSRAFilePath)
#test if file is paired or single end
if pe.is_paired(self.localSRAFilePath):
self.layout = "PAIRED"
else:
self.layout = "SINGLE"
return True
pu.print_info("Downloading " + self.srr_accession + " ...")
#scan for prefetch arguments
prefetchArgsList = [
'-f', '-t', '-l', '-n', '-s', '-R', '-N', '-X', '-o', '-a',
'--ascp-options', '-p', '--eliminate-quals', '-c', '-o', '-O',
'-h', '-V', '-L', '-v', '-q'
]
#ignore location and file name arguments if given
if '-O' in kwargs:
print("Ignoring -O flag." + " location is: " + self.location)
#delete -O parameter
del kwargs['-O']
if '-o' in kwargs:
print("Ignoring -o flag." + " File name is: " + self.srr_accession)
#delete -o parameter
del kwargs['-o']
prefetch_Cmd = ['prefetch']
prefetch_Cmd.extend(pu.parse_unix_args(prefetchArgsList, kwargs))
prefetch_Cmd.extend(['-O', self.location])
prefetch_Cmd.append(self.srr_accession)
cmdStatus = pe.execute_command(prefetch_Cmd,
objectid=self.srr_accession)
if not cmdStatus:
pu.print_boldred("prefetch failed for:" + self.srr_accession)
return False
#validate path exists
if not pu.check_files_exist(self.localSRAFilePath):
pu.print_boldred("Error downloading file. File " +
self.localSRAFilePath + " does not exist!!!")
return False
print("Downloaded file: " + self.localSRAFilePath +
" {0} ".format(pu.get_file_size(self.localSRAFilePath)))
#save file .sra file size
self.sraFileSize = pu.get_file_size(self.localSRAFilePath)
#test if file is paired or single end
if pe.is_paired(self.localSRAFilePath):
self.layout = "PAIRED"
else:
self.layout = "SINGLE"
return True
def download_fastq(self,
verbose=False,
quiet=False,
logs=True,
procs=2,
**kwargs):
"""Function to download fastq files
"""
#check if fastq files exists already
if self.fastqFilesExistsLocally():
pu.print_green("Fastq files exist already")
return True
fasterqdumpArgsList = [
'-f', '-t', '-s', '-N', '-X', '-a', '-p', '-c', '-o', '-O', '-h',
'-V', '-L', '-v', '-q', '-b', '-m', '-x', '-S', '-3', '-P', '-M',
'-B', '--option-file', '--strict', '--table',
'--include-technical', '--skip-technical', '--concatenate-reads'
]
fstrqd_Cmd = ['fasterq-dump']
fstrqd_Cmd.extend(pu.parse_unix_args(fasterqdumpArgsList, kwargs))
#add location
fstrqd_Cmd.extend(['-O', self.location])
#add output filename. output will be <srr_accession>.fastq or <srr_accession>_1.fastq and <srr_accession>_2.fastq
fstrqd_Cmd.extend(['-o', self.srr_accession + ".fastq"])
fstrqd_Cmd.extend(['-e', str(procs)])
if self.sraFileExistsLocally():
fstrqd_Cmd.append(self.localSRAFilePath)
else:
fstrqd_Cmd.append(self.srr_accession)
#execute command
cmdStatus = pe.execute_command(fstrqd_Cmd, objectid=self.srr_accession)
if not cmdStatus:
print("fasterqdump failed for:" + self.srr_accession)
return False
if not hasattr(self, 'layout'):
fq_files = pe.find_files(self.location,
self.srr_accession + "*.fastq")
if len(fq_files) == 1:
self.layout = 'SINGLE'
else:
self.layout = 'PAIRED'
#check if fastq files are downloaded
if (self.layout == "SINGLE"):
self.localfastqPath = os.path.join(self.location,
self.srr_accession + ".fastq")
if not pu.check_files_exist(self.localfastqPath):
pu.print_boldred("Error running fasterq-dump file. File " +
self.localfastqPath + " does not exist!!!")
return False
else:
self.localfastq1Path = os.path.join(
self.location, self.srr_accession + "_1.fastq")
self.localfastq2Path = os.path.join(
self.location, self.srr_accession + "_2.fastq")
if not pu.check_files_exist(self.localfastq1Path,
self.localfastq2Path):
pu.print_boldred("Error running fasterq-dump file. File " +
self.localfastq1Path + " does not exist!!!")
return False
return True
def build_index(self,index_path,transcriptome,objectid="NA"):
"""Function to build kallisto index
index_path: str
path to the index
transcriptome: str
Path to transcriptome
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
:return: Status of kallisto index
:rtype: bool
"""
#if index already exists then exit
if not _force:
#check if files exists
if pu.check_files_exist(index_path):
pu.print_green("Kallisto index {} already exists.".format(index_path))
self.index=index_path
return True
#check input
if not pu.check_files_exist(transcriptome):
pu.print_boldred("{} does not exist. Exiting".format(transcriptome))
raise ValueError("Please check input to kallisto index")
#create out dir
indexdir=pu.get_file_directory(index_path)
#create the out dir
if not pu.check_paths_exist(indexdir):
if not pu.mkdir(indexdir):
raise OSError("Error creating kallisto index. Failed to create index directory.")
args=(transcriptome,)
internal_kwargs={"-i":index_path}
#read build parameters
yamlfile=os.path.join(_params_dir,'kallisto_index.yaml')
if pu.check_files_exist(yamlfile):
yaml_params=pl.YAML_loader(yamlfile)
yaml_kwargs=yaml_params.get_kwargs()
internal_kwargs={**yaml_kwargs,**internal_kwargs}
#add positional args
internal_kwargs['--']=args
validArgsIndex=valid_args._args_KALLISTO_INDEX
kallisto_cmd=['kallisto','index']
kallisto_cmd.extend(pu.parse_unix_args(validArgsIndex,internal_kwargs))
#call kallisto
status=pe.execute_command(kallisto_cmd,objectid=objectid)
if status:
if pu.check_files_exist(index_path) and not _dryrun:
#update object's index
self.index=index_path
if self.check_index():
return True
else:
raise OSError("Error building kallisto index")
return False
def build_index(self,index_path,transcriptome,objectid="NA"):
"""
Parameters
----------
index_path : TYPE
DESCRIPTION.
transcriptome : TYPE
DESCRIPTION.
objectid : TYPE, optional
DESCRIPTION. The default is "NA".
Raises
------
OSError
DESCRIPTION.
Returns
-------
bool
DESCRIPTION.
"""
#if index already exists then exit
if not _force:
#check if files exists
if pu.check_salmonindex(index_path):
pu.print_green("Salmon index {} already exists.".format(index_path))
self.index=index_path
return True
#check input
if not pu.check_files_exist(transcriptome):
pu.print_boldred("{} does not exist. Exiting".format(transcriptome))
return False
#create out dir
indexdir=pu.get_file_directory(index_path)
#create the out dir
if not pu.check_paths_exist(indexdir):
if not pu.mkdir(indexdir):
raise OSError("Error creating salmon index. Failed to create index directory.")
validArgsIndex=valid_args._args_SALMON_INDEX
internal_kwargs={"--threads":_threads,"-t":transcriptome,"-i":index_path}
#read build parameters
yamlfile=os.path.join(_params_dir,'salmon_index.yaml')
if pu.check_files_exist(yamlfile):
yaml_params=pl.YAML_loader(yamlfile)
yaml_kwargs=yaml_params.get_kwargs()
internal_kwargs={**yaml_kwargs,**internal_kwargs}
salmon_cmd=['salmon','index']
salmon_cmd.extend(pu.parse_unix_args(validArgsIndex,internal_kwargs))
#call salmon
status=pe.execute_command(salmon_cmd,objectid=objectid)
if status:
if pu.check_salmonindex(index_path) and not _dryrun:
#update object's index
self.index=index_path
if self.check_index():
return True
else:
raise OSError("Error building salmon index")
return False
def build_index(self, index_path, genome, objectid="NA"):
"""Build a STAR index with given parameters and saves the new index to self.index.
Parameters
----------
index_path: string
Path where the index will be created
genome: string
Path to the reference genome
objectid : string
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
:return: Returns the status of STAR-build index
:rtype: bool
"""
#if index already exists then exit
if not _force:
if pu.check_starindex(index_path):
pu.print_green(
"STAR index {} already exists.".format(index_path))
self.index = index_path
return True
#check input files
if not (pu.check_files_exist(genome)):
pu.print_boldred(
"Please provide a valid input fasta file to build STAR index")
raise ValueError("Please check input to build star index")
#create index path if doesnt exist
if not pu.check_paths_exist(index_path):
if not pu.mkdir(index_path):
raise OSError(
"Error creating STAR index. Failed to create index directory."
)
return False
#determine parameters and execute cmd
#internal_args=()
internal_kwargs = {
"--runMode": "genomeGenerate",
"--genomeDir": index_path,
"--genomeFastaFiles": genome,
"--runThreadN": self._threads
}
#read build parameters
yamlfile = os.path.join(_params_dir, 'star_index.yaml')
if pu.check_files_exist(yamlfile):
yaml_params = pl.YAML_loader(yamlfile)
yaml_kwargs = yaml_params.get_kwargs()
internal_kwargs = {**yaml_kwargs, **internal_kwargs}
starbuild_Cmd = ['STAR']
starbuild_Cmd.extend(
pu.parse_unix_args(valid_args._args_STAR, internal_kwargs))
#execute command
status = pe.execute_command(starbuild_Cmd, objectid=objectid)
if status:
if pu.check_paths_exist(index_path) and not _dryrun:
#update object's index
self.index = index_path
if self.check_index():
return True
else:
raise OSError("Error building STAR index")
return True
def build_index(self, index_path, genome, objectid="NA"):
"""Build a bowtie2 index with given parameters and saves the new index to self.index.
Parameters
----------
index_path: string
Path where the index will be created
genome: string
Path to the reference genome
objectid : string
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
:return: Returns the status of bowtie2-build
:rtype: bool
"""
#check input references
if not _force:
if pu.check_bowtie2index(index_path):
pu.print_green(
"bowtie index {} already exists.".format(index_path))
self.index = index_path
return True
#check input files
if not (pu.check_files_exist(genome)):
pu.print_boldred(
"Please provide a valid input fasta file to build bowtie2 index"
)
raise ValueError("Please check input to star build index")
return False
bowtie2_build_args = [
'-f', '-c', '--large-index', '--debug', '--sanitized', '--verbose',
'-a', '--noauto', '-p', '--packed', '--bmax', '--bmaxdivn',
'--dcv', '--nodc', '-r', '--noref', '-3', '--justref', '-o',
'--offrate', '-t', '--ftabchars', '--threads', '--seed', '-q',
'--quiet'
]
#create the out dir
indexdir = pu.get_file_directory(index_path)
if not pu.check_paths_exist(indexdir):
if not pu.mkdir(indexdir):
raise OSError(
"Error creating bowtie2 index. Failed to create index directory."
)
return False
args = (genome, index_path)
internal_kwargs = {"--threads": self._threads}
#read build parameters
yamlfile = os.path.join(_params_dir, 'bowtie2_index.yaml')
if pu.check_files_exist(yamlfile):
yaml_params = pl.YAML_loader(yamlfile)
yaml_kwargs = yaml_params.get_kwargs()
internal_kwargs = {**yaml_kwargs, **internal_kwargs}
#add positional args
internal_kwargs['--'] = args
bowtie2Build_Cmd = ['bowtie2-build']
#add options
bowtie2Build_Cmd.extend(
pu.parse_unix_args(bowtie2_build_args, internal_kwargs))
#start ececution
status = pe.execute_command(bowtie2Build_Cmd, objectid=objectid)
if not status:
pu.print_boldred("bowtie2-build failed")
return False
if status:
if pu.check_bowtie2index(index_path) and not _dryrun:
#update object's index
self.index = index_path
if self.check_index():
return True
else:
raise OSError("Error building bowtie2 index")
return True
def download_fastq(self,*args,**kwargs):
"""Function to download fastq files
"""
#check if fastq files exists already
if self.fastq_exists():
pu.print_green("Fastq files exist already")
return True
#internal_args are created by pyrpipe and will always replace external passed args
#add the positional args
if self.sra_exists():
internal_args=(self.sra_path,)
else:
#fstrqd_Cmd.append(self.srr_accession)
internal_args=(self.srr_accession,)
#keyword args; boolean flags have empty values
internal_kwargs={'-O':self.directory,
'-o':self.srr_accession+".fastq",
'-e':_threads,
'-f':""
}
#merge args, kwargs, internal_args, internal_kwargs
#If args and kwargs are present
if args or kwargs:
internal_kwargs={**kwargs,**internal_kwargs}
internal_args=tuple(set(args+internal_args))
#append the args to the kwargs using special key '--'
internal_kwargs['--']=internal_args
else:
#check for yaml parameters
filepath=os.path.join(_params_dir,'fasterq-dump.yaml')
yaml_params=pl.YAML_loader(filepath)
yaml_kwargs=yaml_params.get_kwargs()
#yaml_args=yaml_params.get_args()
internal_kwargs={**yaml_kwargs,**internal_kwargs}
#internal_args=tuple(set(yaml_args+internal_args))
internal_kwargs['--']=internal_args
params_list=pu.parse_unix_args(valid_args._args_FASTERQDUMP,internal_kwargs)
fstrqd_Cmd=['fasterq-dump']
#add command and params
fstrqd_Cmd.extend(params_list)
#execute command
cmdStatus=pe.execute_command(fstrqd_Cmd,objectid=self.srr_accession)
if not cmdStatus:
pu.print_boldred("fasterqdump failed for:"+self.srr_accession)
return False
#self.search_fastq(self.directory)
#determine layout
self.layout='PAIRED'
#check files with names <SRR>_1.fastq and <SRR>_2.fastq
fq=os.path.join(self.directory,self.srr_accession+'_1.fastq')
fq2=os.path.join(self.directory,self.srr_accession+'_2.fastq')
self.fastq_path=fq
self.fastq2_path=fq2
#if dry run
if _dryrun: return True
if pu.check_files_exist(fq,fq2):
self.fastq_path=fq
self.fastq2_path=fq2
self.layout="PAIRED"
#remove SRA
self.delete_sra()
return True
#check single end file
fq=os.path.join(self.directory,self.srr_accession+'.fastq')
if pu.check_files_exist(fq):
self.fastq_path=fq
self.layout="SINGLE"
#remove SRA
self.delete_sra()
return True
return False
def run(self,
*args,
subcommand=None,
target=None,
requires=None,
objectid=None,
verbose=None,
logs=None,
**kwargs):
"""
Parameters
----------
*args : Tuple
Positoinal arguments passed to a command. This will copmletely REPLACE the exsiting self._args created during initialization of the runnable object.
subcommand : String or List, optional
DESCRIPTION. subcommand passed to the command. The default is None.
target : Str or List of Str, optional
DESCRIPTION. The expected output/target files produced by the run operation. False is returned is all target files are not found after the command. The default is None.
requires : Str or List of Str, optional
DESCRIPTION. Files required to strat the run method. Exception is thrown if files are missing. The default is None.
objectid : Str, optional
DESCRIPTION. A uniq id to identify the run operation in the logs. Thi is useful for benchmarks. The default is None.
**kwargs : Keyword arguments
DESCRIPTION. The options to be passed to the command. This will OVERRIDE ANY EXISTING options in the self._kwargs created during initialization of the runnable object.
Raises
------
TypeError
If incorerct types are used for target and required.
FileNotFoundError
Raises FileNotFoundError if any of the required files are missing.
OSError
Raises OSError if the command is incorrect or not present in path.
ValueError
Raises ValueError if args_type is something other than LINUX or JAVA.
Returns
-------
bool
Return the status of command as True or False. True implies command had 0 exit-code and all target files were found after the command finished.
"""
#create target list
target_list = []
locks = []
requires_list = []
if target:
if isinstance(target, str):
target_list = [target]
elif isinstance(target, list):
target_list = target
else:
raise TypeError("target must be a string or a list object")
#ckeck for locks and remove previous locks and associated targets if exist
for target in target_list:
self.verify_integrity(target)
#if target already present and not overwrite exists then return
if not _force and target_list:
if self.verify_target_list(target_list):
pu.print_green('Target files {} already exist.'.format(
', '.join(target_list)))
return True
#check if all requirements are satisfied
if requires:
if isinstance(requires, str):
requires_list = [requires]
elif isinstance(requires, list):
requires_list = requires
else:
raise TypeError("requires must be a string or a list object")
#Raise exception if requirements not satisfied
if requires_list:
if not self.verify_target_list(requires_list):
pu.print_boldred('Required files {} fot found.'.format(
', '.join(requires_list)))
raise FileNotFoundError("FilesNotFound")
#check if any required file had lock
for file in requires_list:
if len(self.get_lock_files(file)):
pu.print_boldred(
'Required file {} is corrupt. Please verify file is correct and remove any .Lock files'
.format(', '.join(requires_list)))
raise FileNotFoundError("FilesNotFound")
#override class kwargs by passed kwargs
kwargs = {**self._kwargs, **kwargs}
#if no args provided use constructor's args
if not args:
args = self._args
#if args are not None
if args and args[0]:
kwargs['--'] = args
#make a copy of self._command
if not self._command:
pu.print_boldred("Error: command can not be None or empty")
raise OSError("CommandNotFoundException")
cmd = []
if isinstance(self._command, list):
cmd = self._command.copy()
elif isinstance(self._command, str):
cmd = [self._command]
#if subcommand supplied
#get valid args
valid_args_subcommand = self.get_valid_parameters(subcommand)
if subcommand:
if isinstance(subcommand, str):
subcommand = [subcommand]
#add to command
cmd.extend(subcommand)
#parse and add parameters
if self._args_style == 'LINUX':
cmd.extend(pu.parse_unix_args(valid_args_subcommand, kwargs))
elif self._args_style == 'JAVA':
cmd.extend(pu.parse_java_args(valid_args_subcommand, kwargs))
else:
pu.print_boldred("Unknown args style: {}".format(self._args_style))
raise ValueError("Unknown args style")
#create locks on target; locks indicate incomplete commands
if not _dryrun: locks = self.create_lock(target_list, ' '.join(cmd))
#execute command
cmd_status = pe.execute_command(cmd,
objectid=objectid,
verbose=verbose,
logs=logs)
# if command finished remove locks
self.remove_locks(locks)
if not cmd_status:
pu.print_boldred("{} failed: {}".format(self._command,
" ".join(cmd)))
#remove target files
if not _dryrun and target_list:
pu.print_boldred("Removing target files {}: ".format(
', '.join(target_list)))
pe.delete_files(*target_list)
return False
if cmd_status and target_list and not _dryrun:
return self.verify_target_list(target_list, verbose=True)
#return status
return cmd_status
def build_index(self,
index_path,
*args,
threads=None,
overwrite=False,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Build a star index with given parameters and saves the new index to self.star_index.
Parameters
----------
index_path: string
Path where the index will be created
args: tuple
Path to reference input files
threads: int
Num threads to use
overwrite: bool
Overwrite if index already exists
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
Parameters for the star command
:return: Returns status of star command
:rtype: bool
"""
#if index already exists then exit
if not overwrite:
if pu.check_starindex(index_path):
pu.print_green("STAR index already exists. Using it...")
self.star_index = index_path
return True
#check input files
if len(args) < 1:
pu.print_boldred(
"Please provide input fasta file to build STAR index")
return False
if not pu.check_files_exist(*args):
raise Exception("Please check input to star index")
return False
#create path if doesnt exist
if not pu.check_paths_exist(index_path):
if not pu.mkdir(index_path):
raise Exception("Error creating STAR index. Exiting.")
return False
if not threads:
threads = self.threads
#add runMode
newOpts = {
"--runMode": "genomeGenerate",
"--genomeDir": index_path,
"--genomeFastaFiles": " ".join(args),
"--runThreadN": str(threads)
}
mergedOpts = {**newOpts, **kwargs}
starbuild_Cmd = ['STAR']
starbuild_Cmd.extend(pu.parse_unix_args(None, mergedOpts))
#execute command
status = pe.execute_command(starbuild_Cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if status:
if pu.check_paths_exist(index_path):
#update object's index
self.star_index = index_path
if self.check_index():
return True
else:
return False
def build_index(self,
index_path,
index_name,
*args,
threads=None,
overwrite=False,
verbose=False,
quiet=False,
logs=True,
objectid="NA",
**kwargs):
"""Build a bowtie2 index with given parameters and saves the new index to self.bowtie2_index.
Parameters
----------
index_path: string
Path where the index will be created
index_name: string
A name for the index
args: tuple
Path to reference input files
threads: int
Num threads to use
overwrite: bool
Overwrite already existing index
verbose: bool
Print stdout and std error
quiet: bool
Print nothing
logs: bool
Log this command to pyrpipe logs
objectid: str
Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
kwargs: dict
Options to pass to bowtie2. This will override the existing options in self.passed_args_dict (only replace existing arguments and not replace all the arguments).
:return: Returns the status of bowtie-build
:rtype: bool
"""
#check input references
if len(args) < 1:
pu.print_boldred(
"No reference sequence provided to bowtie2-build. Exiting")
return False
if not pu.check_files_exist(*args):
pu.print_boldred(
"Please check input reference sequences provided to bowtie2-build. Exiting"
)
return False
bowtie2_build_args = [
'-f', '-c', '--large-index', '--debug', '--sanitized', '--verbose',
'-a', '--noauto', '-p', '--packed', '--bmax', '--bmaxdivn',
'--dcv', '--nodc', '-r', '--noref', '-3', '--justref', '-o',
'--offrate', '-t', '--ftabchars', '--threads', '--seed', '-q',
'--quiet', '-h', '--help', '--usage', '--version'
]
#create the out dir
if not pu.check_paths_exist(index_path):
if not pu.mkdir(index_path):
print(
"ERROR in building bowtie2 index. Failed to create index directory."
)
return False
if not overwrite:
#check if files exists
if pu.check_bowtie2index(os.path.join(index_path, index_name)):
print(
"bowtie2 index with same name already exists. Exiting...")
self.bowtie2_index = os.path.join(index_path, index_name)
return True
bowtie2Build_Cmd = ['bowtie2-build']
if not threads:
threads = self.threads
newopts = {"--threads": str(threads)}
mergedopts = {**newopts, **kwargs}
#add options
bowtie2Build_Cmd.extend(
pu.parse_unix_args(bowtie2_build_args, mergedopts))
#add input files
bowtie2Build_Cmd.append(str(",".join(args)))
#add dir/basenae
bowtie2Build_Cmd.append(os.path.join(index_path, index_name))
#print("Executing:"+str(" ".join(hisat2Build_Cmd)))
#start ececution
status = pe.execute_command(bowtie2Build_Cmd,
verbose=verbose,
quiet=quiet,
logs=logs,
objectid=objectid)
if not status:
pu.print_boldred("bowtie2-build failed")
return False
#check index files
if not pu.check_bowtie2index(os.path.join(index_path, index_name)):
pu.print_boldred("bowtie2-build failed")
return False
#set the index path
self.bowtie2_index = os.path.join(index_path, index_name)
#return status
return True