def run_makedb(fasta, db=None, **kwargs):
'''Format database from a fasta file.
This is similar to running ``diamond makedb --in db.faa --db db``.
Parameters
----------
fasta : str
Input path for the fasta file.
db : str or None (default)
Output path for the formatted database file. It will be named
after input file in the same directory by default.
kwargs : dict
keyword arguments. Other command line parameters for diamond makedb.
Returns
-------
`Dumpling`
'''
logger = getLogger(__name__)
if db is None:
db = splitext(fasta)[0]
makedb = Dumpling(['diamond', 'makedb'],
params=Parameters(*makedb_params),
version='0.7.12',
url='https://github.com/bbuchfink/diamond')
makedb.update(fasta=fasta, db=db, **kwargs)
logger.info('Running {}'.format(makedb.command))
makedb()
return makedb
def run_blast(query, daa, aligner='blastp', **kwargs):
'''Search query sequences against the database.
Parameters
----------
query : str
The file path of the query seq
daa : str
The file path of the output daa file
aligner : str
The aligner. blastp or blastx
kwargs : dict
keyword arguments. Command line parameters for diamond blastp
or blastx.
Returns
-------
str
The file path of the blast result.
'''
logger = getLogger(__name__)
blast = Dumpling(['diamond', aligner],
params=Parameters(*blast_params))
blast.update(query=query, daa=daa, **kwargs)
logger.info('Running {}'.format(blast.command))
blast()
return blast
def run(db, query, out_dir, **kwargs):
'''Scan a fasta file against a covariance model database.
Parameters
----------
db : str
The file path to HMM database.
query : str
Input fasta file.
out_dir : str
dir to store output file path of target hits table.
kwargs : dict
Other command line parameters for hmmscan. key is the option
(e.g. "-T") and value is the value for the option (e.g. "50").
If the option is a flag, set the value to None.
Returns
-------
`Dumpling`
'''
logger = getLogger(__name__)
prefix = splitext(basename(query))[0]
out = join(out_dir, '{}.tblout'.format(prefix))
hmmscan = Dumpling('hmmscan', params=Parameters(*_scan_params))
hmmscan.update(query=query, db=db, out=out, **kwargs)
logger.info('Running {}'.format(hmmscan.command))
hmmscan()
return hmmscan
def run(db, query, out_dir, **kwargs):
'''Scan a fasta file against a covariance model database.
Parameters
----------
db : str
The file path to HMM database.
query : str
Input fasta file.
out_dir : str
dir to store output file path of target hits table.
kwargs : dict
Other command line parameters for hmmscan. key is the option
(e.g. "-T") and value is the value for the option (e.g. "50").
If the option is a flag, set the value to None.
Returns
-------
`Dumpling`
'''
logger = getLogger(__name__)
prefix = splitext(basename(query))[0]
out = join(out_dir, '{}.tblout'.format(prefix))
hmmscan = Dumpling('hmmscan', params=Parameters(*_scan_params))
hmmscan.update(query=query, db=db, out=out, **kwargs)
logger.info('Running {}'.format(hmmscan.command))
hmmscan()
return hmmscan
def run(db, query, out_dir, **kwargs):
'''Scan a fasta file against a covariance model database.
Parameters
----------
db : str
The file path to CM database.
query : str
Input fasta file.
out_dir : str
dir to store output file path of target hits table.
kwargs : dict
keyword arguments. command line parameters for cmscan.
Returns
-------
`Dumpling`
'''
logger = getLogger(__name__)
prefix = splitext(basename(query))[0]
out = join(out_dir, '{}.tblout'.format(prefix))
cmscan = Dumpling('cmscan', params=Parameters(*cmscan_params))
cmscan.update(query=query, db=db, out=out, **kwargs)
logger.info('Running {}'.format(cmscan.command))
cmscan()
return cmscan
def run_blast(query, daa, aligner='blastp', **kwargs):
'''Search query sequences against the database.
Parameters
----------
query : str
The file path of the query seq
daa : str
The file path of the output daa file
aligner : str
The aligner. blastp or blastx
kwargs : dict
keyword arguments. Command line parameters for diamond blastp
or blastx.
Returns
-------
str
The file path of the blast result.
'''
logger = getLogger(__name__)
blast = Dumpling(['diamond', aligner], params=Parameters(*blast_params))
blast.update(query=query, daa=daa, **kwargs)
logger.info('Running {}'.format(blast.command))
blast()
return blast
def run_makedb(fasta, db=None, **kwargs):
'''Format database from a fasta file.
This is similar to running ``diamond makedb --in db.faa --db db``.
Parameters
----------
fasta : str
Input path for the fasta file.
db : str or None (default)
Output path for the formatted database file. It will be named
after input file in the same directory by default.
kwargs : dict
keyword arguments. Other command line parameters for diamond makedb.
Returns
-------
`Dumpling`
'''
logger = getLogger(__name__)
if db is None:
db = splitext(fasta)[0]
makedb = Dumpling(['diamond', 'makedb'], params=Parameters(*makedb_params),
version='0.7.12', url='https://github.com/bbuchfink/diamond')
makedb.update(fasta=fasta, db=db, **kwargs)
logger.info('Running {}'.format(makedb.command))
makedb()
return makedb
def run(query, out_dir, cpus=1, **kwargs):
'''Run prodigal for gene prediction.
Notes
-----
It will create 3 output files with prefix of "prodigal" in "out_dir" folder:
1. the annotation file (GFF3 file by default)
2. the nucleotide sequences for each predicted gene
with file suffix of .fna.
3. the protein sequence translated from each gene
with file suffix of .faa.
Parameters
----------
query : str
input file path of sequence
out_dir : str
output dir
cpus : int
Prodigal does not have a param to set up how many CPU cores. This is a fake parameter
to make it conform to the same API with other apps for the sake of convenience.
kwargs : dict
keyword arguments for Prodigal.
Returns
-------
`Dumpling`
'''
logger = getLogger(__name__)
makedirs(out_dir, exist_ok=True)
prodigal = Dumpling('prodigal',
params=Parameters(*params),
version='v2.6.3',
url='https://github.com/hyattpd/Prodigal')
# set default output to gff and run mode to draft genome
prodigal.update(query=query, fmt='gff', mode='single')
# update with kwargs
prodigal.update(**kwargs)
suffices = {
'-a': 'faa',
# output file of nucleotide sequences of genes
'-d': 'fna',
'-o': prodigal.params['fmt'].value
}
for flag in ['-a', '-d', '-o']:
p = prodigal.params[flag]
if p.is_off():
p.on(join(out_dir, 'prodigal.{}'.format(suffices[flag])))
logger.info('Running CDS prediction {}'.format(prodigal.command))
prodigal(stdout=join(out_dir, 'prodigal.log'))
return prodigal
def run(query, out_dir, cpus=1, **kwargs):
"""Run prodigal for gene prediction.
Notes
-----
It will create 3 output files with prefix of "prodigal" in "out_dir" folder:
1. the annotation file (GFF3 file by default)
2. the nucleotide sequences for each predicted gene
with file suffix of .fna.
3. the protein sequence translated from each gene
with file suffix of .faa.
Parameters
----------
query : str
input file path of sequence
out_dir : str
output dir
cpus : int
Prodigal does not have a param to set up how many CPU cores. This is a fake parameter
to make it conform to the same API with other apps for the sake of convenience.
kwargs : dict
keyword arguments for Prodigal.
Returns
-------
`Dumpling`
"""
logger = getLogger(__name__)
makedirs(out_dir, exist_ok=True)
prodigal = Dumpling(
"prodigal", params=Parameters(*params), version="v2.6.3", url="https://github.com/hyattpd/Prodigal"
)
# set default output to gff and run mode to draft genome
prodigal.update(query=query, fmt="gff", mode="single")
# update with kwargs
prodigal.update(**kwargs)
suffices = {
"-a": "faa",
# output file of nucleotide sequences of genes
"-d": "fna",
"-o": prodigal.params["fmt"].value,
}
for flag in ["-a", "-d", "-o"]:
p = prodigal.params[flag]
if p.is_off():
p.on(join(out_dir, "prodigal.{}".format(suffices[flag])))
logger.info("Running CDS prediction {}".format(prodigal.command))
prodigal(stdout=join(out_dir, "prodigal.log"))
return prodigal
def run(query, out_dir, cpus=1, gff=True, **kwargs):
'''Predict CRISPRs for the input file.
Notes
-----
It will create 1 or 2 output files, depending on the parameters:
1. file containing CRIPSR information, including locations of CRISPRs
and their sequence composition OR
GFF file with short information on CRISPR locations OR
GFFFull file with detailed information on CRISPR locations
2. (OPTIONAL; -spacers flag) Fasta file of predicted CRISPR spacers
Parameters
----------
query : str
input file path of nucleotide sequence
out_dir : str
output dir
cpus : int
Minced does not have a param to set up how many CPU cores. This is a fake parameter
to make it conform to the same API with other apps for the sake of convenience.
gff : bool
output in gff3 format
kwargs : dict
keyword arguments. Other command line parameters for MinCED. key is the option
(e.g. "-searchWL") and value is the value for the option (e.g. "6").
If the option is a flag, set the value to None.
Returns
-------
'''
logger = getLogger(__name__)
minced = Dumpling('minced', params=Parameters(*params),
version='0.2.0', url='https://github.com/ctSkennerton/minced')
prefix = splitext(basename(query))[0]
out = join(out_dir, '{}.gff'.format(prefix))
minced.update(query=query, out=out, gff=gff, **kwargs)
logger.info('Running {}'.format(minced.command))
p = minced()
if not exists(out):
# minced raises Java error but return 0 exit code if the input file is invalid,
# so raise the exception for minced manually if no output is created.
p.returncode = 1
raise CalledProcessError(
p.returncode,
cmd=repr(p.args))
return minced
def run(query, out_dir, cpus=1, gff=True, **kwargs):
"""Predict CRISPRs for the input file.
Notes
-----
It will create 1 or 2 output files, depending on the parameters:
1. file containing CRIPSR information, including locations of CRISPRs
and their sequence composition OR
GFF file with short information on CRISPR locations OR
GFFFull file with detailed information on CRISPR locations
2. (OPTIONAL; -spacers flag) Fasta file of predicted CRISPR spacers
Parameters
----------
query : str
input file path of nucleotide sequence
out_dir : str
output dir
cpus : int
Minced does not have a param to set up how many CPU cores. This is a fake parameter
to make it conform to the same API with other apps for the sake of convenience.
gff : bool
output in gff3 format
kwargs : dict
keyword arguments. Other command line parameters for MinCED. key is the option
(e.g. "-searchWL") and value is the value for the option (e.g. "6").
If the option is a flag, set the value to None.
Returns
-------
"""
logger = getLogger(__name__)
minced = Dumpling(
"minced", params=Parameters(*params), version="0.2.0", url="https://github.com/ctSkennerton/minced"
)
prefix = splitext(basename(query))[0]
out = join(out_dir, "{}.gff".format(prefix))
minced.update(query=query, out=out, gff=gff, **kwargs)
logger.info("Running {}".format(minced.command))
p = minced()
if not exists(out):
# minced raises Java error but return 0 exit code if the input file is invalid,
# so raise the exception for minced manually if no output is created.
p.returncode = 1
raise CalledProcessError(p.returncode, cmd=repr(p.args))
return minced
def run_hmmpress(hmm, force=False):
'''Compress the HMM database.
Parameters
----------
hmm : str
The file path to HMM database.
force : boolean
Whether to overwrite.'''
params = [
OptionParam('-f', name='force', help='force overwrite'),
ArgmntParam(name='hmm', help='hmm file to press')]
hmmpress = Dumpling('hmmpress', params=Parameters(*params))
hmmpress.update(hmm=hmm, force=force)
hmmpress()
return hmmpress
def run_cmpress(cm, force=False):
'''Compress the CM database.
Parameters
----------
cm : str
The file path to CM database.
force : boolean
Whether to overwrite.'''
params = [
OptionParam('-F', name='force', help='force overwrite'),
ArgmntParam(name='cm', help='cm file to press')]
cmpress = Dumpling('cmpress', params=Parameters(*params))
cmpress.update(cm=cm, force=force)
cmpress()
return cmpress
def run_view(daa, out, fmt='sam', **kwargs):
'''Convert Diamond daa file to a human readable output.
Parameters
----------
daa : str
Input file resulting from diamond blast.
out : str
Output file.
'''
logger = getLogger(__name__)
view = Dumpling(['diamond', 'view'], params=Parameters(*view_params))
view.update(daa=daa, out=out, fmt=fmt, **kwargs)
logger.info('Running {}'.format(view.command))
view()
return view
def run_hmmpress(hmm, force=False):
'''Compress the HMM database.
Parameters
----------
hmm : str
The file path to HMM database.
force : boolean
Whether to overwrite.'''
params = [
OptionParam('-f', name='force', help='force overwrite'),
ArgmntParam(name='hmm', help='hmm file to press')
]
hmmpress = Dumpling('hmmpress', params=Parameters(*params))
hmmpress.update(hmm=hmm, force=force)
hmmpress()
return hmmpress
def run_view(daa, out, fmt='sam', **kwargs):
'''Convert Diamond daa file to a human readable output.
Parameters
----------
daa : str
Input file resulting from diamond blast.
out : str
Output file.
'''
logger = getLogger(__name__)
view = Dumpling(['diamond', 'view'],
params=Parameters(*view_params))
view.update(daa=daa, out=out, fmt=fmt, **kwargs)
logger.info('Running {}'.format(view.command))
view()
return view
def scan_file(query, db, cpu=1, **kwargs):
cmscan = Dumpling('cmscan', params=Parameters(*_params))
cmscan.update(query=query, db=db, **kwargs)
return cmscan()
def scan_seq(seq, db, cpu=1, **kwargs):
cmscan = Dumpling('cmscan', params=Parameters(*_params))
with NamedTemporaryFile(mode='w+') as i:
write(seq, into=i.name, format='fasta')
cmscan.update(query=i.name, db=db, **kwargs)
return cmscan()