def __init__(self, root_dir, nfl_fa, bas_fofn, ccs_fofn,
ice_opts, sge_opts, hq_isoforms_fa=None, hq_isoforms_fq=None,
lq_isoforms_fa=None, lq_isoforms_fq=None, fasta_fofn=None):
"""
root_dir --- IceFiles.root_dir, usually data/clusterOutDir
nfl_fa --- non-full-length reads in fasta, e.g., isoseq_nfl.fa
bas_fofn --- e.g. input.fofn of bas|bax.h5 files
ccs_fofn --- e.g. reads_of_insert.fofn of ccs files.
hq_isoforms_fa|fq --- polished, hiqh quality consensus isoforms in fasta|q
lq_isoforms_fa|fq --- polished, low quality consensus isoforms in fasta|q
"""
IceFiles.__init__(self, prog_name="IcePolish", root_dir=root_dir,
bas_fofn=bas_fofn, ccs_fofn=ccs_fofn,
fasta_fofn=fasta_fofn)
self.nfl_fa = realpath(nfl_fa)
self.hq_isoforms_fa = hq_isoforms_fa
self.hq_isoforms_fq = hq_isoforms_fq
self.lq_isoforms_fa = lq_isoforms_fa
self.lq_isoforms_fq = lq_isoforms_fq
self.ice_opts = ice_opts
self.sge_opts = sge_opts
self.icep = None # IceAllPartials.
self.iceq = None # IceQuiver
self.icepq = None # IcePostQuiver
self._nfl_splitted_fas = None
self._validate_inputs()
def __init__(self,
root_dir,
fasta_filenames,
ref_fasta,
out_pickle,
sge_opts,
sa_file=None,
ccs_fofn=None):
"""
fasta_filenames --- a list of splitted nfl fasta files.
ref_fasta --- (unpolished) consensus isoforms
out_pickle --- a pickle file with all nfl fasta reads
ccs_fofn --- should be reads_of_insert.fofn or None
root_dir --- ICE root output directory
sge_opts --- params for SGE environment, including
use_sge : use SGE or not
max_sge_jobs: maximum number of gcon jobs submitted
unique_id : unique qsub job id, important that this
DOES NOT CONFLICT!
blasr_nproc: blasr -nproc param, number of threads per cpu.
gcon_nproc : number of gcon that can run at the same time
"""
self.prog_name = "IceAllPartials"
IceFiles.__init__(self, prog_name=self.prog_name, root_dir=root_dir)
self.fasta_filenames, self.ref_fasta, self.ccs_fofn, self.sa_file = \
self._validateInputs(fasta_filenames=fasta_filenames,
ref_fasta=ref_fasta,
ccs_fofn=ccs_fofn,
sa_file=sa_file)
self.out_pickle = out_pickle
self.sge_opts = sge_opts
self.add_log("Making dir for mapping noFL reads: " + self.nfl_dir)
mkdir(self.nfl_dir)
self.add_log("input fasta files are: " +
", ".join(self.fasta_filenames))
self.add_log("temp pickle files are: " +
", ".join(self.pickle_filenames))
self.add_log("out pickle file is: " + self.out_pickle)
def __init__(self,
root_dir,
nfl_fa,
bas_fofn,
ccs_fofn,
ice_opts,
sge_opts,
ipq_opts,
fasta_fofn=None,
nfl_reads_per_split=30000):
"""
root_dir --- IceFiles.root_dir, usually data/clusterOutDir
nfl_fa --- non-full-length reads in fasta, e.g., isoseq_nfl.fa
bas_fofn --- e.g. input.fofn of bas|bax.h5 files
ccs_fofn --- e.g. reads_of_insert.fofn of ccs files.
ipq_opts --- IceQuiverHQLQOptions
qv_trim_5: ignore QV of n bases in the 5' end
qv_trim_3: ignore QV of n bases in the 3' end
hq_quiver_min_accuracy: minimum allowed quiver accuracy
to mark an isoform as high quality
hq_isoforms_fa|fq: polished, hiqh quality consensus
isoforms in fasta|q
lq_isoforms_fa|fq: polished, low quality consensus
isoforms in fasta|q
"""
IceFiles.__init__(self,
prog_name="IcePolish",
root_dir=root_dir,
bas_fofn=bas_fofn,
ccs_fofn=ccs_fofn,
fasta_fofn=fasta_fofn)
self.nfl_fa = realpath(nfl_fa)
self.nfl_reads_per_split = nfl_reads_per_split
self.ice_opts = ice_opts
self.sge_opts = sge_opts
self.ipq_opts = ipq_opts
self.icep = None # IceAllPartials.
self.iceq = None # IceQuiver
self.icepq = None # IceQuiverPostprocess
self._nfl_splitted_fas = None
self.validate_inputs()
def __init__(self, root_dir, fastq_filenames, ref_fasta,
out_pickle, sge_opts, sa_file=None, ccs_fofn=None):
"""
fastq_filenames --- a list of splitted nfl fastq files.
ref_fasta --- (unpolished) consensus isoforms
out_pickle --- a pickle file with all nfl fasta reads
ccs_fofn --- should be reads_of_insert.fofn or None
root_dir --- ICE root output directory
sge_opts --- params for SGE environment, including
use_sge : use SGE or not
max_sge_jobs: maximum number of sub-jobs submitted
unique_id : unique qsub job id, important that this
DOES NOT CONFLICT!
blasr_nproc: blasr -nproc param, number of threads per cpu.
"""
self.prog_name = "IceAllPartials"
IceFiles.__init__(self, prog_name=self.prog_name, root_dir=root_dir)
self.add_log("DEBUG: in IceAllPartials, ccs_fofn is {0}.".format(ccs_fofn), level=logging.INFO)
self.fastq_filenames, self.ref_fasta, self.ccs_fofn, self.sa_file = \
self._validate_inputs(fastq_filenames=fastq_filenames,
ref_fasta=ref_fasta,
ccs_fofn=ccs_fofn,
sa_file=sa_file)
self.out_pickle = out_pickle
self.sge_opts = sge_opts
self.add_log("Making dir for mapping noFL reads: " + self.nfl_dir)
mkdir(self.nfl_dir)
self.add_log("input fasta files are: " +
", ".join(self.fastq_filenames))
self.add_log("temp pickle files are: " +
", ".join(self.pickle_filenames))
self.add_log("out pickle file is: " + self.out_pickle)
def __init__(self,
root_dir,
nfl_fa,
bas_fofn,
ccs_fofn,
ice_opts,
sge_opts,
hq_isoforms_fa=None,
hq_isoforms_fq=None,
lq_isoforms_fa=None,
lq_isoforms_fq=None,
fasta_fofn=None):
"""
root_dir --- IceFiles.root_dir, usually data/clusterOutDir
nfl_fa --- non-full-length reads in fasta, e.g., isoseq_nfl.fa
bas_fofn --- e.g. input.fofn of bas|bax.h5 files
ccs_fofn --- e.g. reads_of_insert.fofn of ccs files.
hq_isoforms_fa|fq --- polished, hiqh quality consensus isoforms in fasta|q
lq_isoforms_fa|fq --- polished, low quality consensus isoforms in fasta|q
"""
IceFiles.__init__(self,
prog_name="IcePolish",
root_dir=root_dir,
bas_fofn=bas_fofn,
ccs_fofn=ccs_fofn,
fasta_fofn=fasta_fofn)
self.nfl_fa = realpath(nfl_fa)
self.hq_isoforms_fa = hq_isoforms_fa
self.hq_isoforms_fq = hq_isoforms_fq
self.lq_isoforms_fa = lq_isoforms_fa
self.lq_isoforms_fq = lq_isoforms_fq
self.ice_opts = ice_opts
self.sge_opts = sge_opts
self.icep = None # IceAllPartials.
self.iceq = None # IceQuiver
self.icepq = None # IcePostQuiver
self._nfl_splitted_fas = None
self._validate_inputs()
def __init__(self, root_dir, nfl_fa, bas_fofn, ccs_fofn,
ice_opts, sge_opts, ipq_opts, fasta_fofn=None, nfl_reads_per_split=30000):
"""
root_dir --- IceFiles.root_dir, usually data/clusterOutDir
nfl_fa --- non-full-length reads in fasta, e.g., isoseq_nfl.fa
bas_fofn --- e.g. input.fofn of bas|bax.h5 files
ccs_fofn --- e.g. reads_of_insert.fofn of ccs files.
ipq_opts --- IceQuiverHQLQOptions
qv_trim_5: ignore QV of n bases in the 5' end
qv_trim_3: ignore QV of n bases in the 3' end
hq_quiver_min_accuracy: minimum allowed quiver accuracy
to mark an isoform as high quality
hq_isoforms_fa|fq: polished, hiqh quality consensus
isoforms in fasta|q
lq_isoforms_fa|fq: polished, low quality consensus
isoforms in fasta|q
"""
IceFiles.__init__(self, prog_name="IcePolish", root_dir=root_dir,
bas_fofn=bas_fofn, ccs_fofn=ccs_fofn,
fasta_fofn=fasta_fofn)
#self.add_log("DEBUG: in Polish ccs_fofn is {0}".format(self.ccs_fofn))
#self.add_log("DEBUG: in Polish fasta_fofn is {0}".format(self.fasta_fofn))
#self.add_log("DEBUG: in Polish bas_fofn is {0}".format(self.bas_fofn))
self.nfl_fa = realpath(nfl_fa)
self.nfl_reads_per_split = nfl_reads_per_split
self.ice_opts = ice_opts
self.sge_opts = sge_opts
self.ipq_opts = ipq_opts
self.add_log("ece_penalty: {0}, ece_min_len: {1}".format(self.ice_opts.ece_penalty, self.ice_opts.ece_min_len))
self.icep = None # IceAllPartials.
self.iceq = None # IceQuiver
self.icepq = None # IceQuiverPostprocess
self._nfl_splitted_fas = None
self.validate_inputs()
