def resolved_tool_contract_runner(rtc):
"""
For each cluster bin, create summary.json, cluster_report.csv,
hq_isoforms.fa|fq, lq_isoforms.fa|fq
Finally, merge all cluster bins and save all outputs to 'combined'.
"""
p = ChunkTasksPickle.read(rtc.task.input_files[0])
assert all([isinstance(task, ClusterChunkTask) for task in p])
p.sorted_by_attr(attr='cluster_bin_index')
opts = rtc.task.options
ipq_opts = IceQuiverHQLQOptions(
qv_trim_5=opts[Constants.QV_TRIM_FIVEPRIME_ID],
qv_trim_3=opts[Constants.QV_TRIM_THREEPRIME_ID],
hq_quiver_min_accuracy=opts[Constants.HQ_QUIVER_MIN_ACCURACY_ID])
sample_name = get_sample_name(
input_sample_name=opts[Constants.SAMPLE_NAME_ID])
out_consensus_isoforms_cs = rtc.task.output_files[0]
out_summary = rtc.task.output_files[1]
out_report = rtc.task.output_files[2]
out_hq_cs = rtc.task.output_files[3]
out_hq_fq = rtc.task.output_files[4]
out_lq_cs = rtc.task.output_files[5]
out_lq_fq = rtc.task.output_files[6]
out_hq_lq_prefix_dict_pickle = rtc.task.output_files[7]
assert out_consensus_isoforms_cs.endswith(".contigset.xml")
assert out_hq_cs.endswith(".contigset.xml")
assert out_lq_cs.endswith(".contigset.xml")
out_consensus_isoforms_fa = out_consensus_isoforms_cs.replace(
".contigset.xml", ".fasta")
out_hq_fa = out_hq_cs.replace('.contigset.xml', '.fasta')
out_lq_fa = out_lq_cs.replace('.contigset.xml', '.fasta')
hq_fq_fns, lq_fq_fns = [], []
split_uc_pickles, split_partial_uc_pickles = [], []
split_consensus_isoforms = []
cluster_bin_indices = [task.cluster_bin_index for task in p]
cluster_out_dirs = [task.cluster_out_dir for task in p]
# sanity check that Cluster indices are unique!
assert len(set(cluster_bin_indices)) == len(cluster_bin_indices)
for task in p:
ice_pq = IceQuiverPostprocess(root_dir=task.cluster_out_dir,
ipq_opts=ipq_opts)
hq_fq_fns.append(ice_pq.quivered_good_fq)
lq_fq_fns.append(ice_pq.quivered_bad_fq)
split_uc_pickles.append(ice_pq.final_pickle_fn)
split_partial_uc_pickles.append(ice_pq.nfl_all_pickle_fn)
split_consensus_isoforms.append(ice_pq.final_consensus_fa)
combined_dir = op.join(op.dirname(op.dirname(cluster_out_dirs[0])),
"combined")
mkdir(combined_dir)
combined_files = CombinedFiles(combined_dir)
log.info("Combining results of all cluster bins to %s.", combined_dir)
log.info("Merging HQ|LQ isoforms from all cluster bins.")
log.info("HQ isoforms are: %s.", ",".join(hq_fq_fns))
log.info("LQ isoforms are: %s.", ",".join(lq_fq_fns))
combine_polished_isoforms(
split_indices=cluster_bin_indices,
split_hq_fns=hq_fq_fns,
split_lq_fns=lq_fq_fns,
combined_hq_fa=combined_files.all_hq_fa,
combined_hq_fq=combined_files.all_hq_fq,
combined_lq_fa=combined_files.all_lq_fa,
combined_lq_fq=combined_files.all_lq_fq,
hq_lq_prefix_dict_pickle=combined_files.hq_lq_prefix_dict_pickle,
sample_name=sample_name)
ln(combined_files.all_hq_fa, out_hq_fa) #'HQ isoforms'
ln(combined_files.all_hq_fq, out_hq_fq) #'HQ isoforms'
ln(combined_files.all_lq_fa, out_lq_fa) #'LQ isoforms'
ln(combined_files.all_lq_fq, out_lq_fq) #'LQ isoforms'
ln(combined_files.hq_lq_prefix_dict_pickle, out_hq_lq_prefix_dict_pickle)
as_contigset(out_hq_fa, out_hq_cs)
as_contigset(out_lq_fa, out_lq_cs)
log.info("Merging consensus isoforms from all cluster bins.")
combine_consensus_isoforms(split_indices=cluster_bin_indices,
split_files=split_consensus_isoforms,
combined_consensus_isoforms_fa=combined_files.
all_consensus_isoforms_fa,
sample_name=sample_name)
ln(combined_files.all_consensus_isoforms_fa, out_consensus_isoforms_fa)
#consensus isoforms
as_contigset(out_consensus_isoforms_fa, out_consensus_isoforms_cs)
log.info("Writing cluster summary to %s",
combined_files.all_cluster_summary_fn)
write_cluster_summary(summary_fn=combined_files.all_cluster_summary_fn,
isoforms_fa=out_consensus_isoforms_cs,
hq_fa=out_hq_fa,
lq_fa=out_lq_fa)
ln(combined_files.all_cluster_summary_fn, out_summary) # "cluster summary"
log.info("Writing cluster report to %s",
combined_files.all_cluster_report_fn)
write_combined_cluster_report(
split_indices=cluster_bin_indices,
split_uc_pickles=split_uc_pickles,
split_partial_uc_pickles=split_partial_uc_pickles,
report_fn=combined_files.all_cluster_report_fn,
sample_name=sample_name)
ln(combined_files.all_cluster_report_fn, out_report) # "cluster report"
def resolved_tool_contract_runner(rtc):
"""
For each cluster bin, create summary.json, cluster_report.csv,
hq_isoforms.fa|fq, lq_isoforms.fa|fq
Finally, merge all cluster bins and save all outputs to 'combined'.
"""
p = ChunkTasksPickle.read(rtc.task.input_files[0])
assert all([isinstance(task, ClusterChunkTask) for task in p])
p.sorted_by_attr(attr='cluster_bin_index')
opts = rtc.task.options
ipq_opts = IceQuiverHQLQOptions(qv_trim_5=opts[Constants.QV_TRIM_FIVEPRIME_ID],
qv_trim_3=opts[Constants.QV_TRIM_THREEPRIME_ID],
hq_quiver_min_accuracy=opts[Constants.HQ_QUIVER_MIN_ACCURACY_ID])
sample_name = get_sample_name(input_sample_name=opts[Constants.SAMPLE_NAME_ID])
out_consensus_isoforms_cs = rtc.task.output_files[0]
out_summary = rtc.task.output_files[1]
out_report = rtc.task.output_files[2]
out_hq_cs = rtc.task.output_files[3]
out_hq_fq = rtc.task.output_files[4]
out_lq_cs = rtc.task.output_files[5]
out_lq_fq = rtc.task.output_files[6]
out_hq_lq_prefix_dict_pickle = rtc.task.output_files[7]
assert out_consensus_isoforms_cs.endswith(".contigset.xml")
assert out_hq_cs.endswith(".contigset.xml")
assert out_lq_cs.endswith(".contigset.xml")
out_consensus_isoforms_fa = out_consensus_isoforms_cs.replace(".contigset.xml", ".fasta")
out_hq_fa = out_hq_cs.replace('.contigset.xml', '.fasta')
out_lq_fa = out_lq_cs.replace('.contigset.xml', '.fasta')
hq_fq_fns, lq_fq_fns = [], []
split_uc_pickles, split_partial_uc_pickles = [], []
split_consensus_isoforms = []
cluster_bin_indices = [task.cluster_bin_index for task in p]
cluster_out_dirs = [task.cluster_out_dir for task in p]
# sanity check that Cluster indices are unique!
assert len(set(cluster_bin_indices)) == len(cluster_bin_indices)
for task in p:
ice_pq = IceQuiverPostprocess(root_dir=task.cluster_out_dir,
ipq_opts=ipq_opts)
hq_fq_fns.append(ice_pq.quivered_good_fq)
lq_fq_fns.append(ice_pq.quivered_bad_fq)
split_uc_pickles.append(ice_pq.final_pickle_fn)
split_partial_uc_pickles.append(ice_pq.nfl_all_pickle_fn)
split_consensus_isoforms.append(ice_pq.final_consensus_fa)
combined_dir = op.join(op.dirname(op.dirname(cluster_out_dirs[0])), "combined")
mkdir(combined_dir)
combined_files = CombinedFiles(combined_dir)
log.info("Combining results of all cluster bins to %s.", combined_dir)
log.info("Merging HQ|LQ isoforms from all cluster bins.")
log.info("HQ isoforms are: %s.", ",".join(hq_fq_fns))
log.info("LQ isoforms are: %s.", ",".join(lq_fq_fns))
combine_polished_isoforms(split_indices=cluster_bin_indices,
split_hq_fns=hq_fq_fns,
split_lq_fns=lq_fq_fns,
combined_hq_fa=combined_files.all_hq_fa,
combined_hq_fq=combined_files.all_hq_fq,
combined_lq_fa=combined_files.all_lq_fa,
combined_lq_fq=combined_files.all_lq_fq,
hq_lq_prefix_dict_pickle=combined_files.hq_lq_prefix_dict_pickle,
sample_name=sample_name)
ln(combined_files.all_hq_fa, out_hq_fa) #'HQ isoforms'
ln(combined_files.all_hq_fq, out_hq_fq) #'HQ isoforms'
ln(combined_files.all_lq_fa, out_lq_fa) #'LQ isoforms'
ln(combined_files.all_lq_fq, out_lq_fq) #'LQ isoforms'
ln(combined_files.hq_lq_prefix_dict_pickle, out_hq_lq_prefix_dict_pickle)
as_contigset(out_hq_fa, out_hq_cs)
as_contigset(out_lq_fa, out_lq_cs)
log.info("Merging consensus isoforms from all cluster bins.")
combine_consensus_isoforms(split_indices=cluster_bin_indices,
split_files=split_consensus_isoforms,
combined_consensus_isoforms_fa=combined_files.all_consensus_isoforms_fa,
sample_name=sample_name)
ln(combined_files.all_consensus_isoforms_fa, out_consensus_isoforms_fa)
#consensus isoforms
as_contigset(out_consensus_isoforms_fa, out_consensus_isoforms_cs)
log.info("Writing cluster summary to %s", combined_files.all_cluster_summary_fn)
write_cluster_summary(summary_fn=combined_files.all_cluster_summary_fn,
isoforms_fa=out_consensus_isoforms_cs,
hq_fa=out_hq_fa,
lq_fa=out_lq_fa)
ln(combined_files.all_cluster_summary_fn, out_summary) # "cluster summary"
log.info("Writing cluster report to %s", combined_files.all_cluster_report_fn)
write_combined_cluster_report(split_indices=cluster_bin_indices,
split_uc_pickles=split_uc_pickles,
split_partial_uc_pickles=split_partial_uc_pickles,
report_fn=combined_files.all_cluster_report_fn,
sample_name=sample_name)
ln(combined_files.all_cluster_report_fn, out_report) # "cluster report"
def test_get_sample_name(self):
"""Test get_sample_name"""
self.assertTrue(get_sample_name("my_name"), "my_name")
self.assertTrue(get_sample_name("my name,|"), "myname")
self.assertTrue(len(get_sample_name("")) > 0)
def args_runner(args):
"""args runner"""
logging.info("%s arguments are:\n%s\n", __file__, args)
# sanity check arguments
_sanity_check_args(args)
# make option objects
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,
flnc_reads_per_split=args.flnc_reads_per_split,
nfl_reads_per_split=args.nfl_reads_per_split)
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)
# (1) separate flnc reads into bins
logging.info("Separating FLNC reads into bins.")
tofu_f = TofuFiles(tofu_dir=args.tofu_dir)
s = SeparateFLNCRunner(flnc_fa=args.flnc_fa,
root_dir=args.tofu_dir,
out_pickle=tofu_f.separate_flnc_pickle,
bin_size_kb=args.bin_size_kb,
bin_by_primer=args.bin_by_primer,
bin_manual=args.bin_manual,
max_base_limit_MB=args.max_base_limit_MB)
s.run()
flnc_files = SeparateFLNCBase.convert_pickle_to_sorted_flnc_files(
tofu_f.separate_flnc_pickle)
logging.info("Separated FLNC reads bins are %s", flnc_files)
# (2) apply 'pbtranscript cluster' to each bin
# run ICE/Quiver (the whole thing), providing the fasta_fofn
logging.info("Running ICE/Polish on separated FLNC reads bins.")
split_dirs = []
for flnc_file in flnc_files:
split_dir = op.join(realpath(op.dirname(flnc_file)), "cluster_out")
mkdir(split_dir)
split_dirs.append(split_dir)
cur_out_cons = op.join(split_dir, "consensus_isoforms.fasta")
ipq_f = IceQuiverPostprocess(root_dir=split_dir, ipq_opts=ipq_opts)
if op.exists(ipq_f.quivered_good_fq):
logging.warning("HQ polished isoforms %s already exist. SKIP!",
ipq_f.quivered_good_fq)
continue
else:
logging.info("Running ICE/Quiver on %s", split_dir)
rmpath(cur_out_cons)
obj = Cluster(root_dir=split_dir,
flnc_fa=flnc_file,
nfl_fa=args.nfl_fa,
bas_fofn=args.bas_fofn,
ccs_fofn=args.ccs_fofn,
fasta_fofn=args.fasta_fofn,
out_fa=cur_out_cons,
sge_opts=sge_opts,
ice_opts=ice_opts,
ipq_opts=ipq_opts)
if args.mem_debug: # DEBUG
from memory_profiler import memory_usage
start_t = time.time()
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(
split_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()
if not args.keep_tmp_files: # by deafult, delete all tempory files.
logging.info("Deleting %s", ipq_f.tmp_dir)
subprocess.Popen(['rm', '-rf', '%s' % ipq_f.tmp_dir])
logging.info("Deleting %s", ipq_f.quivered_dir)
subprocess.Popen(['rm', '-rf', '%s' % ipq_f.quivered_dir])
# (3) merge polished isoform cluster from all bins
logging.info("Merging isoforms from all bins to %s.", tofu_f.combined_dir)
c = CombineRunner(combined_dir=tofu_f.combined_dir,
sample_name=get_sample_name(args.sample_name),
split_dirs=split_dirs,
ipq_opts=ipq_opts)
c.run()
if args.summary_fn is not None:
ln(tofu_f.all_cluster_summary_fn, args.summary_fn)
if args.report_fn is not None:
ln(tofu_f.all_cluster_report_fn, args.report_fn)
# (4) map HQ isoforms to GMAP reference genome
map_isoforms_and_sort(input_filename=tofu_f.all_hq_fq,
sam_filename=tofu_f.sorted_gmap_sam,
gmap_db_dir=args.gmap_db,
gmap_db_name=args.gmap_name,
gmap_nproc=args.gmap_nproc)
# (5) post mapping to genome analysis, including
# * collapse polished HQ isoform clusters into groups
# * count abundance of collapsed isoform groups
# * filter collapsed isoforms based on abundance info
logging.info("Post mapping to genome analysis.")
out_isoforms = args.collapsed_filtered_fn
if any(out_isoforms.endswith(ext) for ext in (".fa", ".fasta")):
in_isoforms = tofu_f.all_hq_fa
elif any(out_isoforms.endswith(ext) for ext in (".fq", ".fastq")):
in_isoforms = tofu_f.all_hq_fq
else:
raise ValueError("Output file %s must be FASTA or FASTQ!" %
out_isoforms)
post_mapping_to_genome_runner(in_isoforms=in_isoforms,
in_sam=tofu_f.sorted_gmap_sam,
in_pickle=tofu_f.hq_lq_prefix_dict_pickle,
out_isoforms=args.collapsed_filtered_fn,
out_gff=args.gff_fn,
out_abundance=args.abundance_fn,
out_group=args.group_fn,
out_read_stat=args.read_stat_fn,
min_aln_coverage=args.min_aln_coverage,
min_aln_identity=args.min_aln_identity,
min_flnc_coverage=args.min_flnc_coverage,
max_fuzzy_junction=args.max_fuzzy_junction,
allow_extra_5exon=args.allow_extra_5exon,
min_count=args.min_count)
return 0
def args_runner(args):
"""args runner"""
logging.info("%s arguments are:\n%s\n", __file__, args)
# sanity check arguments
_sanity_check_args(args)
# make option objects
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,
nfl_reads_per_split=args.nfl_reads_per_split)
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)
# (1) separate flnc reads into bins
logging.info("Separating FLNC reads into bins.")
tofu_f = TofuFiles(tofu_dir=args.tofu_dir)
s = SeparateFLNCRunner(flnc_fa=args.flnc_fa, root_dir=args.tofu_dir,
out_pickle=tofu_f.separate_flnc_pickle,
bin_size_kb=args.bin_size_kb, bin_by_primer=args.bin_by_primer,
bin_manual=args.bin_manual, max_base_limit_MB=args.max_base_limit_MB)
s.run()
flnc_files = SeparateFLNCBase.convert_pickle_to_sorted_flnc_files(tofu_f.separate_flnc_pickle)
logging.info("Separated FLNC reads bins are %s", flnc_files)
# (2) apply 'pbtranscript cluster' to each bin
# run ICE/Quiver (the whole thing), providing the fasta_fofn
logging.info("Running ICE/Polish on separated FLNC reads bins.")
split_dirs = []
for flnc_file in flnc_files:
split_dir = op.join(realpath(op.dirname(flnc_file)), "cluster_out")
mkdir(split_dir)
split_dirs.append(split_dir)
cur_out_cons = op.join(split_dir, "consensus_isoforms.fasta")
ipq_f = IceQuiverPostprocess(root_dir=split_dir, ipq_opts=ipq_opts)
if op.exists(ipq_f.quivered_good_fq):
logging.warning("HQ polished isoforms %s already exist. SKIP!", ipq_f.quivered_good_fq)
continue
else:
logging.info("Running ICE/Quiver on %s", split_dir)
rmpath(cur_out_cons)
obj = Cluster(root_dir=split_dir, flnc_fa=flnc_file,
nfl_fa=args.nfl_fa,
bas_fofn=args.bas_fofn,
ccs_fofn=args.ccs_fofn,
fasta_fofn=args.fasta_fofn,
out_fa=cur_out_cons, sge_opts=sge_opts,
ice_opts=ice_opts, ipq_opts=ipq_opts)
if args.mem_debug: # DEBUG
from memory_profiler import memory_usage
start_t = time.time()
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(split_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()
if not args.keep_tmp_files: # by deafult, delete all tempory files.
logging.info("Deleting %s", ipq_f.tmp_dir)
subprocess.Popen(['rm', '-rf', '%s' % ipq_f.tmp_dir])
logging.info("Deleting %s", ipq_f.quivered_dir)
subprocess.Popen(['rm', '-rf', '%s' % ipq_f.quivered_dir])
# (3) merge polished isoform cluster from all bins
logging.info("Merging isoforms from all bins to %s.", tofu_f.combined_dir)
c = CombineRunner(combined_dir=tofu_f.combined_dir,
sample_name=get_sample_name(args.sample_name),
split_dirs=split_dirs, ipq_opts=ipq_opts)
c.run()
if args.summary_fn is not None:
ln(tofu_f.all_cluster_summary_fn, args.summary_fn)
if args.report_fn is not None:
ln(tofu_f.all_cluster_report_fn, args.report_fn)
# (4) map HQ isoforms to GMAP reference genome
map_isoforms_and_sort(input_filename=tofu_f.all_hq_fq, sam_filename=tofu_f.sorted_gmap_sam,
gmap_db_dir=args.gmap_db, gmap_db_name=args.gmap_name,
gmap_nproc=args.gmap_nproc)
# (5) post mapping to genome analysis, including
# * collapse polished HQ isoform clusters into groups
# * count abundance of collapsed isoform groups
# * filter collapsed isoforms based on abundance info
logging.info("Post mapping to genome analysis.")
out_isoforms = args.collapsed_filtered_fn
if any(out_isoforms.endswith(ext) for ext in (".fa", ".fasta")):
in_isoforms = tofu_f.all_hq_fa
elif any(out_isoforms.endswith(ext) for ext in (".fq", ".fastq")):
in_isoforms = tofu_f.all_hq_fq
else:
raise ValueError("Output file %s must be FASTA or FASTQ!" % out_isoforms)
post_mapping_to_genome_runner(
in_isoforms=in_isoforms, in_sam=tofu_f.sorted_gmap_sam,
in_pickle=tofu_f.hq_lq_prefix_dict_pickle, out_isoforms=args.collapsed_filtered_fn,
out_gff=args.gff_fn, out_abundance=args.abundance_fn,
out_group=args.group_fn, out_read_stat=args.read_stat_fn,
min_aln_coverage=args.min_aln_coverage, min_aln_identity=args.min_aln_identity,
min_flnc_coverage=args.min_flnc_coverage, max_fuzzy_junction=args.max_fuzzy_junction,
allow_extra_5exon=args.allow_extra_5exon, min_count=args.min_count)
return 0
def run(self):
"""
For each cluster bin, create summary.json, cluster_report.csv,
hq_isoforms.fa|fq, lq_isoforms.fa|fq
Finally, merge all cluster bins and save all outputs to 'combined'.
"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=self.getVersion()))
args = self.args
# Get cluster bins directories as input
cluster_bin_dirs = self.get_cluster_bin_dirs(separate_flnc_pickle=args.separate_flnc_pickle,
cluster_bin_dirs=args.cluster_bin_dirs)
cluster_bin_indices = range(0, len(cluster_bin_dirs))
# Create output dir
combined_dir = args.combined_dir
mkdir(combined_dir)
# Get combined output filenames
def f(input_fn, default_fn):
if input_fn is None:
return op.join(combined_dir, default_fn)
out_consensus_isoforms_fa = f(args.consensus_isoforms_fa, "all.consensus_isoforms.fasta")
out_summary = f(args.summary_fn, "all.cluster_summary.json")
out_report = f(args.report_fn, "all.cluster_report.csv")
out_hq_fa = f(args.hq_isoforms_fa, "all.polished_hq.fasta")
out_lq_fa = f(args.lq_isoforms_fa, "all.polished_lq.fasta")
out_hq_fq = f(args.hq_isoforms_fq, "all.polished_hq.fastq")
out_lq_fq = f(args.lq_isoforms_fq, "all.polished_lq.fastq")
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)
sample_name = get_sample_name(input_sample_name=args.sample_name)
hq_fq_fns, lq_fq_fns = [], []
split_uc_pickles, split_partial_uc_pickles = [], []
split_consensus_isoforms = []
for cluster_bin_dir in cluster_bin_dirs:
ice_pq = IceQuiverPostprocess(root_dir=cluster_bin_dir, ipq_opts=ipq_opts)
hq_fq_fns.append(ice_pq.quivered_good_fq)
lq_fq_fns.append(ice_pq.quivered_bad_fq)
split_uc_pickles.append(ice_pq.final_pickle_fn)
split_partial_uc_pickles.append(ice_pq.nfl_all_pickle_fn)
split_consensus_isoforms.append(ice_pq.final_consensus_fa)
combined_files = CombinedFiles(combined_dir)
log.info("Combining results of all cluster bins to %s.", combined_dir)
log.info("Merging HQ|LQ isoforms from all cluster bins.")
log.info("HQ isoforms are: %s.", ",".join(hq_fq_fns))
log.info("LQ isoforms are: %s.", ",".join(lq_fq_fns))
combine_polished_isoforms(split_indices=cluster_bin_indices,
split_hq_fns=hq_fq_fns,
split_lq_fns=lq_fq_fns,
combined_hq_fa=combined_files.all_hq_fa,
combined_hq_fq=combined_files.all_hq_fq,
combined_lq_fa=combined_files.all_lq_fa,
combined_lq_fq=combined_files.all_lq_fq,
hq_lq_prefix_dict_pickle=combined_files.hq_lq_prefix_dict_pickle,
sample_name=sample_name)
ln(combined_files.all_hq_fa, out_hq_fa) #'HQ isoforms'
ln(combined_files.all_hq_fq, out_hq_fq) #'HQ isoforms'
ln(combined_files.all_lq_fa, out_lq_fa) #'LQ isoforms'
ln(combined_files.all_lq_fq, out_lq_fq) #'LQ isoforms'
log.info("Merging consensus isoforms from all cluster bins.")
combine_consensus_isoforms(split_indices=cluster_bin_indices,
split_files=split_consensus_isoforms,
combined_consensus_isoforms_fa=combined_files.all_consensus_isoforms_fa,
sample_name=sample_name)
ln(combined_files.all_consensus_isoforms_fa, out_consensus_isoforms_fa)
log.info("Writing cluster summary to %s", combined_files.all_cluster_summary_fn)
write_cluster_summary(summary_fn=combined_files.all_cluster_summary_fn,
isoforms_fa=out_consensus_isoforms_fa,
hq_fa=out_hq_fa, lq_fa=out_lq_fa)
ln(combined_files.all_cluster_summary_fn, out_summary) # "cluster summary"
log.info("Writing cluster report to %s", combined_files.all_cluster_report_fn)
write_combined_cluster_report(split_indices=cluster_bin_indices,
split_uc_pickles=split_uc_pickles,
split_partial_uc_pickles=split_partial_uc_pickles,
report_fn=combined_files.all_cluster_report_fn,
sample_name=sample_name)
ln(combined_files.all_cluster_report_fn, out_report) # "cluster report"