def run(self):
"""Execute ice_partial.py all|split|i|merge."""
cmd = self.args.subCommand
logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__),
cmd=cmd,
v=get_version()))
cmd_str = ""
try:
args = self.args
obj = None
if cmd == "all":
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc)
obj = IceAllPartials(
root_dir=args.root_dir,
fasta_filenames=args.fasta_filenames.split(','),
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
sge_opts=sge_opts,
sa_file=args.sa_file,
ccs_fofn=args.ccs_fofn)
elif cmd == "one":
# Only assign nfl reads in the given input_fasta file to isoforms
obj = IcePartialOne(input_fasta=args.input_fasta,
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
sa_file=args.sa_file,
ccs_fofn=args.ccs_fofn,
done_filename=args.done_filename,
blasr_nproc=args.blasr_nproc,
use_finer_qv=args.use_finer_qv)
elif cmd == "split":
obj = IcePartialSplit(root_dir=args.root_dir,
nfl_fa=args.nfl_fa,
N=args.N)
elif cmd == "i":
obj = IcePartialI(root_dir=args.root_dir,
i=args.i,
ccs_fofn=args.ccs_fofn,
blasr_nproc=args.blasr_nproc)
elif cmd == "merge":
obj = IcePartialMerge(root_dir=args.root_dir, N=args.N)
else:
raise ValueError(
"Unknown command passed to {f}: {cmd}.".format(
f=op.basename(__file__), cmd=cmd))
cmd_str = obj.cmd_str()
logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str))
obj.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".format(
cmd_str=cmd_str))
return 1
return 0
def run(self):
"""Execute ice_partial.py all|split|i|merge."""
cmd = self.args.subCommand
logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__),
cmd=cmd, v=get_version()))
cmd_str = ""
try:
args = self.args
obj = None
if cmd == "all":
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc)
obj = IceAllPartials(root_dir=args.root_dir,
fasta_filenames=args.fasta_filenames.split(','),
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
sge_opts=sge_opts,
sa_file=args.sa_file,
ccs_fofn=args.ccs_fofn)
elif cmd == "one":
# Only assign nfl reads in the given input_fastq file to isoforms
obj = IcePartialOne(input_fastq=args.input_fastq,
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
sa_file=args.sa_file,
ccs_fofn=args.ccs_fofn,
done_filename=args.done_filename,
blasr_nproc=args.blasr_nproc,
use_finer_qv=args.use_finer_qv)
elif cmd == "split":
obj = IcePartialSplit(root_dir=args.root_dir,
nfl_fa=args.nfl_fa,
N=args.N)
elif cmd == "i":
obj = IcePartialI(root_dir=args.root_dir, i=args.i,
ccs_fofn=args.ccs_fofn,
blasr_nproc=args.blasr_nproc)
elif cmd == "merge":
obj = IcePartialMerge(root_dir=args.root_dir,
N=args.N)
else:
raise ValueError("Unknown command passed to {f}: {cmd}.".
format(f=op.basename(__file__), cmd=cmd))
cmd_str = obj.cmd_str()
logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str))
obj.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".
format(cmd_str=cmd_str))
return 1
return 0
def run(self):
"""Run"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
args = self.args
try:
convert_fofn_to_fasta(fofn_filename=args.input_fofn,
out_filename=args.fasta_fofn,
fasta_out_dir=args.fasta_out_dir,
force_overwrite=False)
except Exception as e:
logging.error(str(e))
return 1
return 0
def run(self):
"""Run"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
cmd_str = ""
try:
args = self.args
iceqm = IceQuiverMerge(root_dir=args.root_dir, N=args.N)
cmd_str = iceqm.cmd_str()
iceqm.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".
format(cmd_str=cmd_str))
return 1
return 0
def run(self):
"""Run"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
cmd_str = ""
try:
args = self.args
iceqm = IceQuiverMerge(root_dir=args.root_dir, N=args.N)
cmd_str = iceqm.cmd_str()
iceqm.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".format(
cmd_str=cmd_str))
return 1
return 0
def main():
"""Main function, split a fasta into smaller chunks."""
import logging
from pbtools.pbtranscript.__init__ import get_version
log = logging.getLogger(__name__)
args = get_args()
from pbtools.pbtranscript.Utils import setup_log
setup_log(alog=log, level=logging.DEBUG)
log.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
splitFasta(input_fasta=args.input_fasta,
reads_per_split=args.reads_per_split,
out_dir=args.out_dir,
out_prefix=args.out_prefix)
def main():
"""Main function, split a fasta into smaller chunks."""
import logging
from pbtools.pbtranscript.__init__ import get_version
log = logging.getLogger(__name__)
args = get_args()
from pbtools.pbtranscript.Utils import setup_log
setup_log(alog=log, level=logging.DEBUG)
log.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
splitFasta(input_fasta=args.input_fasta,
reads_per_split=args.reads_per_split,
out_dir=args.out_dir,
out_prefix=args.out_prefix)
def set_parser():
"""Set up and return argument parser."""
parser = ArgumentParser()
parser.add_argument("input_fasta",
help="Input fasta filename")
parser.add_argument("output_prefix",
help="Output filename prefix (ex: g_consensus)")
parser.add_argument("consensus_id",
help="Consensus sequence ID name (ex: consensus)")
parser.add_argument("--nproc",
default=8, type=int,
help="Number of processes")
parser.add_argument("--maxScore", default=-1000, type=int,
help="blasr maxScore")
parser.add_argument("--version", "-v",
action='version', version='%(prog)s ' + get_version())
return parser
def set_parser():
"""Set up and return argument parser."""
parser = ArgumentParser()
parser.add_argument("input_fasta", help="Input fasta filename")
parser.add_argument("output_prefix",
help="Output filename prefix (ex: g_consensus)")
parser.add_argument("consensus_id",
help="Consensus sequence ID name (ex: consensus)")
parser.add_argument("--nproc",
default=8,
type=int,
help="Number of processes")
parser.add_argument("--maxScore",
default=-1000,
type=int,
help="blasr maxScore")
parser.add_argument("--version",
"-v",
action='version',
version='%(prog)s ' + get_version())
return parser
def run(self):
"""Execute ice_fa2fq.py."""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
cmd_str = ""
try:
args = self.args
in_fa, ccs_fofn, out_fq = args.in_fa, args.ccs_fofn, \
args.out_fq
self.validate_inputs(in_fa=in_fa, ccs_fofn=ccs_fofn)
cmd_str = self.cmd_str(in_fa=in_fa,
ccs_fofn=ccs_fofn,
out_fq=out_fq)
ice_fa2fq(in_fa=in_fa, ccs_fofn=ccs_fofn, out_fq=out_fq)
except:
logging.exception(
"Exiting {cmd} with return code 1.".format(cmd=cmd_str))
return 1
return 0
def run(self):
"""Execute ice_fa2fq.py."""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
cmd_str = ""
try:
args = self.args
in_fa, ccs_fofn, out_fq = args.in_fa, args.ccs_fofn, \
args.out_fq
self.validate_inputs(in_fa=in_fa,
ccs_fofn=ccs_fofn)
cmd_str = self.cmd_str(in_fa=in_fa, ccs_fofn=ccs_fofn,
out_fq=out_fq)
ice_fa2fq(in_fa=in_fa, ccs_fofn=ccs_fofn, out_fq=out_fq)
except:
logging.exception("Exiting {cmd} with return code 1.".
format(cmd=cmd_str))
return 1
return 0
def tofu_wrap_main():
parser = argparse.ArgumentParser(prog='tofu_wrap')
add_cluster_arguments(parser, show_sge_env_name=True, show_sge_queue=True)
parser.add_argument("--bin_size_kb", default=1, type=int, help="Bin size by kb (default: 1)")
parser.add_argument("--bin_manual", default=None, help="Bin manual (ex: (1,2,3,5)), overwrites bin_size_kb")
parser.add_argument("--bin_by_primer", default=False, action="store_true", help="Instead of binning by size, bin by primer (overwrites --bin_size_kb and --bin_manual)")
parser.add_argument("--max_base_limit_MB", default=600, type=int, help="Maximum number of bases per partitioned bin, in MB (default: 600)")
parser.add_argument("--gmap_name", default="hg19", help="GMAP DB name (default: hg19)")
parser.add_argument("--gmap_db", default="/home/UNIXHOME/etseng/share/gmap_db_new/", help="GMAP DB location (default: /home/UNIXHOME/etseng/share/gmap_db_new/)")
parser.add_argument("--output_seqid_prefix", type=str, default=None, help="Output seqid prefix. If not given, a random ID is generated")
parser.add_argument("--mem_debug", default=False, action="store_true", help=argparse.SUPPRESS)
parser.add_argument("--max_fuzzy_junction", default=5, type=int, help="Max fuzzy junction (default: 5 bp)")
parser.add_argument("--version", action='version', version='%(prog)s ' + str(get_version()))
args = parser.parse_args()
# PRINT VERSION AND EXIT
# if args.version:
# print >> sys.stderr, get_version()
# sys.exit(0)
# DEBUG
if args.mem_debug:
from memory_profiler import memory_usage
# #################################################################
# SANITY CHECKS
if not args.quiver:
print >> sys.stderr, "--quiver must be turned on for tofu_wrap. Quit."
sys.exit(-1)
if args.nfl_fa is None:
print >> sys.stderr, "--nfl_fa must be provided for tofu_wrap. Quit."
sys.exit(-1)
if not os.path.exists(args.gmap_db):
print >> sys.stderr, "GMAP DB location not valid: {0}. Quit.".format(args.gmap_db)
sys.exit(-1)
if not os.path.exists(os.path.join(args.gmap_db, args.gmap_name)):
print >> sys.stderr, "GMAP name not valid: {0}. Quit.".format(args.gmap_name)
sys.exit(-1)
# #################################################################
tofu_prefix = binascii.b2a_hex(os.urandom(3)) if args.output_seqid_prefix is None else args.output_seqid_prefix
ice_opts = IceOptions(quiver=args.quiver,
use_finer_qv=args.use_finer_qv,
targeted_isoseq=args.targeted_isoseq,
ece_penalty=args.ece_penalty,
ece_min_len=args.ece_min_len,
)
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc,
quiver_nproc=args.quiver_nproc,
gcon_nproc=args.gcon_nproc,
sge_env_name=args.sge_env_name,
sge_queue=args.sge_queue)
ipq_opts = IceQuiverHQLQOptions(qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_quiver_min_accuracy=args.hq_quiver_min_accuracy,
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq)
# ex: all_quivered_hq.100_30_0.99.fastq
quiver_hq_filename = "all_quivered_hq.{0}_{1}_{2:.2f}.fastq".format(\
args.qv_trim_5,args.qv_trim_3,args.hq_quiver_min_accuracy)
quiver_lq_filename = "all_quivered_lq.fastq"
# (1) separate input flnc into size bins or primers
if args.bin_by_primer:
split_files = sep_flnc_by_primer(args.flnc_fa, os.path.abspath(args.root_dir))
else:
bin_manual = eval(args.bin_manual) if args.bin_manual is not None else None
split_files = sep_flnc_by_size(args.flnc_fa, args.root_dir, bin_size_kb=args.bin_size_kb, bin_manual=bin_manual, max_base_limit_MB=args.max_base_limit_MB)
print >> sys.stderr, "split input {0} into {1} bins".format(args.flnc_fa, len(split_files))
# (2) if fasta_fofn already is there, use it; otherwise make it first
if args.quiver and args.fasta_fofn is None:
print >> sys.stderr, "Making fasta_fofn now"
nfl_dir = os.path.abspath(os.path.join(args.root_dir, "fasta_fofn_files"))
if not os.path.exists(nfl_dir):
os.makedirs(nfl_dir)
args.fasta_fofn = os.path.join(nfl_dir, 'input.fasta.fofn')
print >> sys.stderr, "fasta_fofn", args.fasta_fofn
print >> sys.stderr, "nfl_dir", nfl_dir
convert_fofn_to_fasta(fofn_filename=args.bas_fofn,
out_filename=args.fasta_fofn,
fasta_out_dir=nfl_dir,
cpus=args.blasr_nproc)
else:
if not os.path.exists(args.fasta_fofn):
raise Exception, "fasta_fofn {0} does not exist!".format(args.fasta_fofn)
for line in open(args.fasta_fofn):
file = line.strip()
if len(file) > 0 and not os.path.exists(file):
raise Exception, "File {0} does not exists in {1}".format(file, args.fasta_fofn)
# (3) run ICE/Quiver (the whole thing), providing the fasta_fofn
split_dirs = []
for cur_file in split_files:
cur_dir = os.path.abspath(os.path.dirname(cur_file))
split_dirs.append(cur_dir)
cur_out_cons = os.path.join(cur_dir, args.consensusFa)
hq_quiver = os.path.join(cur_dir, quiver_hq_filename)
if os.path.exists(hq_quiver):
print >> sys.stderr, "{0} already exists. SKIP!".format(hq_quiver)
continue
print >> sys.stderr, "running ICE/Quiver on", cur_dir
start_t = time.time()
obj = Cluster(root_dir=cur_dir,
flnc_fa=cur_file,
nfl_fa=realpath(args.nfl_fa),
bas_fofn=realpath(args.bas_fofn),
ccs_fofn=realpath(args.ccs_fofn),
fasta_fofn=realpath(args.fasta_fofn),
out_fa=cur_out_cons,
sge_opts=sge_opts,
ice_opts=ice_opts,
ipq_opts=ipq_opts,
report_fn=args.report_fn,
summary_fn=args.summary_fn,
nfl_reads_per_split=args.nfl_reads_per_split)
# DEBUG
if args.mem_debug:
mem_usage = memory_usage(obj.run, interval=60)
end_t = time.time()
with open('mem_debug.log', 'a') as f:
f.write("Running ICE/Quiver on {0} took {1} secs.\n".format(cur_dir, end_t-start_t))
f.write("Maximum memory usage: {0}\n".format(max(mem_usage)))
f.write("Memory usage: {0}\n".format(mem_usage))
else:
obj.run()
combined_dir = os.path.join(args.root_dir, 'combined')
if not os.path.exists(combined_dir):
os.makedirs(combined_dir)
# (4) combine quivered HQ/LQ results
hq_filename, lq_filename, hq_pre_dict, lq_pre_dict = \
combine_quiver_results(split_dirs, combined_dir, quiver_hq_filename, quiver_lq_filename,\
tofu_prefix)
with open(os.path.join(args.root_dir, 'combined', 'combined.hq_lq_pre_dict.pickle'), 'w') as f:
dump({'HQ': hq_pre_dict, 'LQ': lq_pre_dict}, f)
# (5) collapse quivered HQ results
collapse_prefix_hq = run_collapse_sam(hq_filename, args.gmap_db, args.gmap_name, cpus=args.blasr_nproc, max_fuzzy_junction=args.max_fuzzy_junction, dun_merge_5_shorter=True)
# (6) make abundance
get_abundance(collapse_prefix_hq, hq_pre_dict, collapse_prefix_hq)
# (7) run filtering & removing subsets in no5merge
if args.targeted_isoseq:
run_filtering_by_count(collapse_prefix_hq, collapse_prefix_hq+'.min_fl_5', min_count=5)
run_filtering_away_subsets(collapse_prefix_hq+'.min_fl_5', collapse_prefix_hq+'.min_fl_5.filtered', args.max_fuzzy_junction)
else:
run_filtering_by_count(collapse_prefix_hq, collapse_prefix_hq+'.min_fl_2', min_count=2)
run_filtering_away_subsets(collapse_prefix_hq+'.min_fl_2', collapse_prefix_hq+'.min_fl_2.filtered', args.max_fuzzy_junction)
def getVersion(self):
return get_version()
def tofu_wrap_main():
parser = argparse.ArgumentParser(prog='tofu_wrap')
add_cluster_arguments(parser, show_sge_env_name=True, show_sge_queue=True)
parser.add_argument("--bin_size_kb", default=1, type=int, help="Bin size by kb (default: 1)")
parser.add_argument("--bin_manual", default=None, help="Bin manual (ex: (1,2,3,5)), overwrites bin_size_kb")
parser.add_argument("--bin_by_primer", default=False, action="store_true", help="Instead of binning by size, bin by primer (overwrites --bin_size_kb and --bin_manual)")
parser.add_argument("--max_base_limit_MB", default=600, type=int, help="Maximum number of bases per partitioned bin, in MB (default: 600)")
parser.add_argument("--gmap_name", default="hg19", help="GMAP DB name (default: hg19)")
parser.add_argument("--gmap_db", default="/home/UNIXHOME/etseng/share/gmap_db_new/", help="GMAP DB location (default: /home/UNIXHOME/etseng/share/gmap_db_new/)")
parser.add_argument("--output_seqid_prefix", type=str, default=None, help="Output seqid prefix. If not given, a random ID is generated")
parser.add_argument("--mem_debug", default=False, action="store_true", help=argparse.SUPPRESS)
parser.add_argument("--max_fuzzy_junction", default=5, type=int, help="Max fuzzy junction (default: 5 bp)")
parser.add_argument("--version", action='version', version='%(prog)s ' + str(get_version()))
args = parser.parse_args()
# PRINT VERSION AND EXIT
# if args.version:
# print >> sys.stderr, get_version()
# sys.exit(0)
# DEBUG
if args.mem_debug:
from memory_profiler import memory_usage
# #################################################################
# SANITY CHECKS
if not args.quiver:
print >> sys.stderr, "--quiver must be turned on for tofu_wrap. Quit."
sys.exit(-1)
if args.nfl_fa is None:
print >> sys.stderr, "--nfl_fa must be provided for tofu_wrap. Quit."
sys.exit(-1)
if not os.path.exists(args.gmap_db):
print >> sys.stderr, "GMAP DB location not valid: {0}. Quit.".format(args.gmap_db)
sys.exit(-1)
if not os.path.exists(os.path.join(args.gmap_db, args.gmap_name)):
print >> sys.stderr, "GMAP name not valid: {0}. Quit.".format(args.gmap_name)
sys.exit(-1)
# #################################################################
tofu_prefix = binascii.b2a_hex(os.urandom(3)) if args.output_seqid_prefix is None else args.output_seqid_prefix
ice_opts = IceOptions(quiver=args.quiver,
use_finer_qv=args.use_finer_qv,
targeted_isoseq=args.targeted_isoseq,
ece_penalty=args.ece_penalty,
ece_min_len=args.ece_min_len,
)
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc,
quiver_nproc=args.quiver_nproc,
gcon_nproc=args.gcon_nproc,
sge_env_name=args.sge_env_name,
sge_queue=args.sge_queue)
ipq_opts = IceQuiverHQLQOptions(qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_quiver_min_accuracy=args.hq_quiver_min_accuracy,
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq)
# ex: all_quivered_hq.100_30_0.99.fastq
quiver_hq_filename = "all_quivered_hq.{0}_{1}_{2:.2f}.fastq".format(\
args.qv_trim_5,args.qv_trim_3,args.hq_quiver_min_accuracy)
quiver_lq_filename = "all_quivered_lq.fastq"
# (1) separate input flnc into size bins or primers
if args.bin_by_primer:
split_files = sep_flnc_by_primer(args.flnc_fa, os.path.abspath(args.root_dir))
else:
bin_manual = eval(args.bin_manual) if args.bin_manual is not None else None
split_files = sep_flnc_by_size(args.flnc_fa, args.root_dir, bin_size_kb=args.bin_size_kb, bin_manual=bin_manual, max_base_limit_MB=args.max_base_limit_MB)
print >> sys.stderr, "split input {0} into {1} bins".format(args.flnc_fa, len(split_files))
# (2) if fasta_fofn already is there, use it; otherwise make it first
if args.quiver and args.fasta_fofn is None:
print >> sys.stderr, "Making fasta_fofn now"
nfl_dir = os.path.abspath(os.path.join(args.root_dir, "fasta_fofn_files"))
if not os.path.exists(nfl_dir):
os.makedirs(nfl_dir)
args.fasta_fofn = os.path.join(nfl_dir, 'input.fasta.fofn')
print >> sys.stderr, "fasta_fofn", args.fasta_fofn
print >> sys.stderr, "nfl_dir", nfl_dir
convert_fofn_to_fasta(fofn_filename=args.bas_fofn,
out_filename=args.fasta_fofn,
fasta_out_dir=nfl_dir,
cpus=args.blasr_nproc)
else:
if not os.path.exists(args.fasta_fofn):
raise Exception, "fasta_fofn {0} does not exist!".format(args.fasta_fofn)
for line in open(args.fasta_fofn):
file = line.strip()
if len(file) > 0 and not os.path.exists(file):
raise Exception, "File {0} does not exists in {1}".format(file, args.fasta_fofn)
# (3) run ICE/Quiver (the whole thing), providing the fasta_fofn
split_dirs = []
for cur_file in split_files:
cur_dir = os.path.abspath(os.path.dirname(cur_file))
split_dirs.append(cur_dir)
cur_out_cons = os.path.join(cur_dir, args.consensusFa)
hq_quiver = os.path.join(cur_dir, quiver_hq_filename)
if os.path.exists(hq_quiver):
print >> sys.stderr, "{0} already exists. SKIP!".format(hq_quiver)
continue
print >> sys.stderr, "running ICE/Quiver on", cur_dir
start_t = time.time()
obj = Cluster(root_dir=cur_dir,
flnc_fa=cur_file,
nfl_fa=realpath(args.nfl_fa),
bas_fofn=realpath(args.bas_fofn),
ccs_fofn=realpath(args.ccs_fofn),
fasta_fofn=realpath(args.fasta_fofn),
out_fa=cur_out_cons,
sge_opts=sge_opts,
ice_opts=ice_opts,
ipq_opts=ipq_opts,
report_fn=args.report_fn,
summary_fn=args.summary_fn,
nfl_reads_per_split=args.nfl_reads_per_split)
# DEBUG
if args.mem_debug:
mem_usage = memory_usage(obj.run, interval=60)
end_t = time.time()
with open('mem_debug.log', 'a') as f:
f.write("Running ICE/Quiver on {0} took {1} secs.\n".format(cur_dir, end_t-start_t))
f.write("Maximum memory usage: {0}\n".format(max(mem_usage)))
f.write("Memory usage: {0}\n".format(mem_usage))
else:
obj.run()
combined_dir = os.path.join(args.root_dir, 'combined')
if not os.path.exists(combined_dir):
os.makedirs(combined_dir)
# (4) combine quivered HQ/LQ results
hq_filename, lq_filename, hq_pre_dict, lq_pre_dict = \
combine_quiver_results(split_dirs, combined_dir, quiver_hq_filename, quiver_lq_filename,\
tofu_prefix)
with open(os.path.join(args.root_dir, 'combined', 'combined.hq_lq_pre_dict.pickle'), 'w') as f:
dump({'HQ': hq_pre_dict, 'LQ': lq_pre_dict}, f)
# (5) collapse quivered HQ results
collapse_prefix_hq = run_collapse_sam(hq_filename, args.gmap_db, args.gmap_name, cpus=args.blasr_nproc, max_fuzzy_junction=args.max_fuzzy_junction)
# (6) make abundance
get_abundance(collapse_prefix_hq, hq_pre_dict, collapse_prefix_hq)
# (7) run filtering
run_filtering_by_count(collapse_prefix_hq, collapse_prefix_hq+'.min_fl_2', min_count=2)
def run(self):
"""Execute ice_quiver.py all|i|merge|postprocess."""
cmd = self.args.subCommand
logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__),
cmd=cmd, v=get_version()))
cmd_str = ""
try:
args = self.args
obj = None
if cmd == "all":
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc,
quiver_nproc=args.quiver_nproc)
ipq_opts = IceQuiverHQLQOptions(
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq,
qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_quiver_min_accuracy=args.hq_quiver_min_accuracy)
obj = IceQuiverAll(root_dir=args.root_dir,
bas_fofn=args.bas_fofn,
fasta_fofn=args.fasta_fofn,
sge_opts=sge_opts,
ipq_opts=ipq_opts)
elif cmd == "i":
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc,
quiver_nproc=args.quiver_nproc)
obj = IceQuiverI(root_dir=args.root_dir, i=args.i, N=args.N,
bas_fofn=args.bas_fofn,
fasta_fofn=args.fasta_fofn,
sge_opts=sge_opts)
elif cmd == "merge":
obj = IceQuiverMerge(root_dir=args.root_dir, N=args.N)
elif cmd == "postprocess":
ipq_opts = IceQuiverHQLQOptions(
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq,
qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_quiver_min_accuracy=args.hq_quiver_min_accuracy)
obj = IceQuiverPostprocess(root_dir=args.root_dir,
ipq_opts=ipq_opts,
use_sge=args.use_sge,
quit_if_not_done=args.quit_if_not_done,
summary_fn=args.summary_fn,
report_fn=args.report_fn)
else:
raise ValueError("Unknown command passed to {f}: {cmd}.".
format(f=op.basename(__file__), cmd=cmd))
cmd_str = obj.cmd_str()
logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str))
obj.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".
format(cmd_str=cmd_str))
return 1
return 0
def getVersion(self):
"""Return version string."""
return get_version()
def run(self):
"""Execute ice_quiver.py all|i|merge|postprocess."""
cmd = self.args.subCommand
logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__),
cmd=cmd,
v=get_version()))
cmd_str = ""
try:
args = self.args
obj = None
if cmd == "all":
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc,
quiver_nproc=args.quiver_nproc)
ipq_opts = IceQuiverHQLQOptions(
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq,
qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_quiver_min_accuracy=args.hq_quiver_min_accuracy)
obj = IceQuiverAll(root_dir=args.root_dir,
bas_fofn=args.bas_fofn,
fasta_fofn=args.fasta_fofn,
sge_opts=sge_opts,
ipq_opts=ipq_opts)
elif cmd == "i":
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc,
quiver_nproc=args.quiver_nproc)
obj = IceQuiverI(root_dir=args.root_dir,
i=args.i,
N=args.N,
bas_fofn=args.bas_fofn,
fasta_fofn=args.fasta_fofn,
sge_opts=sge_opts)
elif cmd == "merge":
obj = IceQuiverMerge(root_dir=args.root_dir, N=args.N)
elif cmd == "postprocess":
ipq_opts = IceQuiverHQLQOptions(
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq,
qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_quiver_min_accuracy=args.hq_quiver_min_accuracy)
obj = IceQuiverPostprocess(
root_dir=args.root_dir,
ipq_opts=ipq_opts,
use_sge=args.use_sge,
quit_if_not_done=args.quit_if_not_done,
summary_fn=args.summary_fn,
report_fn=args.report_fn)
else:
raise ValueError(
"Unknown command passed to {f}: {cmd}.".format(
f=op.basename(__file__), cmd=cmd))
cmd_str = obj.cmd_str()
logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str))
obj.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".format(
cmd_str=cmd_str))
return 1
return 0
def _logConfigs(self):
"""Log configuration."""
with open(self.configFN, "w", 0) as f:
f.write("pbtranscript " + get_version() + "\n")
f.write(str(self.ice_opts) + "\n")
f.write(str(self.sge_opts) + "\n")
def _logConfigs(self):
"""Log configuration."""
with open(self.configFN, 'w', 0) as f:
f.write('pbtranscript ' + get_version() + "\n")
f.write(str(self.ice_opts) + "\n")
f.write(str(self.sge_opts) + "\n")
def getVersion(self):
"""Get version string"""
return get_version()
def getVersion(self):
"""Get version string"""
return get_version()
def getVersion(self):
return get_version()
def getVersion(self):
"""Return version string."""
return get_version()
