def setup_merged_samples(flist, sample_group_fn=_group_samples, **kw):
"""Setup analysis that merges multiple sample runs.
:param flist: list of file names, by default *-bcbb-config.yaml files
:param sample_group_fn: function that groups files into samples and sample runs. The function takes flist as input.
:returns: updated flist with config files for merged samples
"""
new_flist = []
sample_d = sample_group_fn(flist)
for k, v in sample_d.iteritems():
if len(v) > 1:
f = v[v.keys()[0]]
out_d = os.path.join(os.path.dirname(os.path.dirname(f)), MERGED_SAMPLE_OUTPUT_DIR)
LOG.info("Sample {} has {} sample runs; setting up merge analysis in {}".format(k, len(v), out_d))
dry_makedir(out_d, dry_run=False)
pp = kw.get("post_process") if kw.get("post_process", None) else f.replace("-bcbb-config.yaml", "-post_process.yaml")
with open(pp) as fh:
conf = yaml.load(fh)
conf = update_pp_platform_args(conf, **{'jobname': "{}_total".format(k), 'workdir': out_d, 'output': "{}_total-bcbb.log".format(k) })
pp_new = os.path.join(out_d, os.path.basename(pp))
dry_unlink(pp_new, dry_run=kw.get('dry_run', True))
dry_write(pp_new, yaml.safe_dump(conf, default_flow_style=False, allow_unicode=True, width=1000), dry_run=kw.get('dry_run', True))
# Setup merged bcbb-config file
bcbb_config = merge_sample_config(v.values(), sample=k, out_d=out_d, dry_run=kw.get('dry_run', True))
bcbb_config_file = os.path.join(out_d, os.path.basename(v.values()[0]))
bcbb_config = sort_sample_config_fastq(bcbb_config)
if not os.path.exists(bcbb_config_file) or kw.get('new_config', False):
dry_unlink(bcbb_config_file, dry_run=kw.get('dry_run', True))
dry_write(bcbb_config_file, yaml.safe_dump(bcbb_config, default_flow_style=False, allow_unicode=True, width=1000), dry_run=kw.get('dry_run', True))
##new_flist.extend(v.values())
new_flist.extend([bcbb_config_file])
return new_flist
def _purge_by_sample(files, dry_run, fsize=MINFILESIZE):
saved_size = 0
for i in range(0, len(files)-1):
f1 = os.path.basename(files[i])
f2 = os.path.basename(files[i+1])
if f2.startswith(os.path.splitext(f1)[0]):
statinfo = os.stat(files[i])
if statinfo.st_size < fsize:
continue
saved_size = saved_size + statinfo.st_size
LOG.info("Purging bam file {}".format(files[i]))
dry_unlink(files[i], dry_run)
dry_write(files[i], "File removed to save disk space: Moved to {}".format(files[i+1]), dry_run)
return saved_size
def run_halo(path=None, project=None, batch_size=8, **kw):
"""Run halo application. Setup parameter files and call
halo_pipeline.sh script.
:param project: project name
:param batch_size: number of samples to run in each project config file
"""
plist = sorted(find_samples(path, **kw))
plist_chunks=[plist[x:x+batch_size] for x in xrange(0, len(plist), batch_size)]
i = 0
param_list = []
for pl in plist_chunks:
i += 1
outfile = os.path.join(path, "{}_{}_halo.projectrc".format(project, i))
param = {'cl':None, 'platform_args':None, 'workingDirectory':None}
label = '{}_halo_{}'.format(project[0:3].replace(".", "_"), i)
d = {'samples' : '"{}"'.format(" ".join([os.path.basename(x) for x in pl])),
'indir' : path,
'baits_file' : kw.get('baits', ""),
'targets_file' : kw.get('targets', ""),
'target_region' : kw.get('target_region', ""),
'output' : os.path.join(os.path.dirname(outfile), "{}.out".format(label)),
'error' : os.path.join(os.path.dirname(outfile), "{}.err".format(label))
}
if kw.get("setup", False):
dry_write(outfile, PROJECTTEMPLATE.render(**d), dry_run=kw.get("dry_run", False))
if not os.path.exists(outfile):
LOG.warn("No such configuration file {}; rerun command with '--setup' option")
return []
if kw.get("config", None) and os.path.basename(outfile) != kw.get("config", None):
continue
param['cl'] = [HALOSCRIPT, "-c", HALORC, outfile]
param['platform_args'] = ['--output', os.path.join("{}.out".format(label)),
'--error', os.path.join("{}.err".format(label)),
'--job-name', label]
param['workingDirectory'] = os.path.dirname(outfile)
param_list.append(param)
return param_list
def setup_sample(f, analysis, amplicon=False, genome_build="hg19", **kw):
"""Setup config files, making backups and writing new files
:param path: root path in which to search for samples
:param dry_run: dry run flag
"""
if not os.path.exists(f):
return
with open(f) as fh:
config = yaml.load(fh)
## Check for correctly formatted config
if not config.get("details", None):
LOG.warn("Couldn't find 'details' section in config file {}: aborting setup!".format(f))
return
## Save file to backup if backup doesn't exist
f_bak = f.replace("-bcbb-config.yaml", "-bcbb-config.yaml.bak")
if not os.path.exists(f_bak):
LOG.info("Making backup of {} in {}".format(f, f_bak))
dry_backup(os.path.abspath(f), dry_run=kw['dry_run'])
## Save command file to backup if it doesn't exist
cmdf = f.replace("-bcbb-config.yaml", "-bcbb-command.txt")
if os.path.exists(cmdf):
cmdf_bak = cmdf.replace("-bcbb-command.txt", "-bcbb-command.txt.bak")
if not os.path.exists(cmdf_bak):
LOG.info("Making backup of {} in {}".format(cmdf, cmdf_bak))
dry_backup(os.path.abspath(cmdf), dry_run=kw['dry_run'])
## Save post_process file to backup if it doesn't exist
ppf = f.replace("-bcbb-config.yaml", "-post_process.yaml")
if os.path.exists(ppf):
ppf_bak = ppf.replace("-post_process.yaml", "-post_process.yaml.bak")
if not os.path.exists(ppf_bak):
LOG.info("Making backup of {} in {}".format(ppf, ppf_bak))
dry_backup(ppf, dry_run=kw['dry_run'])
if analysis:
config = update_sample_config(config, "analysis", analysis)
if genome_build:
config = update_sample_config(config, "genome_build", genome_build)
config = sort_sample_config_fastq(config)
## Remove config file and rewrite
dry_unlink(f, kw['dry_run'])
dry_write(f, yaml.safe_dump(config, default_flow_style=False, allow_unicode=True, width=1000), dry_run=kw['dry_run'])
## Setup post process only if not provided at command line
if not kw.get("post_process", None):
ppfile = f.replace("-bcbb-config.yaml", "-post_process.yaml")
with open(ppfile) as fh:
pp = yaml.load(fh)
## Need to set working directory to path of bcbb-config.yaml file
if pp.get('distributed', {}).get('platform_args', None):
platform_args = pp['distributed']['platform_args'].split()
if "-D" in platform_args:
platform_args[platform_args.index("-D")+1] = os.path.dirname(f)
elif "--workdir" in platform_args:
platform_args[platform_args.index("--workdir")+1] = os.path.dirname(f)
pp['distributed']['platform_args'] = " ".join(platform_args)
## Change keys for all analyses
for anl in pp.get('custom_algorithms',{}).keys():
if kw.get('baits', None):
pp['custom_algorithms'][anl]['hybrid_bait'] = kw['baits']
if kw.get('targets', None):
pp['custom_algorithms'][anl]['hybrid_target'] = kw['targets']
if amplicon:
pp['custom_algorithms'][anl]['mark_duplicates'] = False
if amplicon:
LOG.info("setting amplicon analysis")
pp['algorithm']['mark_duplicates'] = False
if kw.get('galaxy_config', None):
pp['galaxy_config'] = kw['galaxy_config']
if kw.get('distributed', None):
LOG.info("setting distributed execution")
pp['algorithm']['num_cores'] = 'messaging'
else:
LOG.info("setting parallell execution")
pp['algorithm']['num_cores'] = kw['num_cores']
if kw.get('snpEff', None):
LOG.info("setting snpEff to {}".format(kw["snpEff"]))
pp['program']['snpEff'] = kw['snpEff']
dry_unlink(ppfile, dry_run=kw['dry_run'])
dry_write(ppfile, yaml.safe_dump(pp, default_flow_style=False, allow_unicode=True, width=1000), dry_run=kw['dry_run'])
def purge_alignments(path, ftype="sam", keep="last", dry_run=False, force=False, fsize=MINFILESIZE):
"""Cleanup sam and bam files. In some cases, sam files persist. If
the corresponding bam file exists, replace the sam file contents
with a message that the file has been removed to save space.
In general, several bam files are produced in an analysis. By
grouping bam files by prefix, either the most recent file is
retained for further reference, or a specific analysis is kept.
"""
if ftype == "sam":
pattern = ".sam$"
elif ftype == "bam":
pattern = ".bam$"
else:
LOG.warn("ftype must be one of 'sam' or 'bam'")
return
LOG.debug("running purge_alignments in path {} with pattern {} keep rule {}".format(path, pattern, keep))
def purge_filter(f):
if not pattern:
return
return re.search(pattern, f) != None
flist = filtered_walk(path, purge_filter, exclude_dirs=["realign-split"])
if len(flist) == 0:
LOG.info("No {} files found in {}".format(ftype, path))
return
if len(flist) > 0 and not query_yes_no("Going to remove/cleanup {} {} files ({}...). Are you sure you want to continue?".format(len(flist), ftype, ",".join([os.path.basename(x) for x in flist[0:10]])), force=force):
return
if ftype == "sam":
for f in flist:
LOG.info("Purging {} file {}".format(ftype, f))
dry_unlink(f, dry_run)
if os.path.exists(f.replace(".sam", ".bam")):
dry_write(f, "File removed to save disk space: SAM converted to BAM", dry_run)
return
elif ftype == "bam":
samples = {}
for f in flist:
m = re.search("([0-9A-Za-z\_]+)-.*", os.path.basename(f))
if not m:
LOG.debug("Couldn't determine prefix for {}".format(f))
continue
sid = m.groups()[0]
if not sid in samples.keys():
samples[sid] = {}
dname = os.path.dirname(f)
if not dname in samples[sid].keys():
samples[sid][dname] = []
samples[sid][dname].append(f)
saved_size = 0
for k in samples.iterkeys():
for d, files in samples[k].iteritems():
if not files or len(files) == 1:
continue
files.sort(lambda x,y: cmp(len(x), len(y)))
if keep == "last":
LOG.info("Keeping file {} and removing all files with common prefix: {}".format(os.path.basename(files[len(files)-1]), ", ".join([os.path.basename(x) for x in files[0:-1]])))
saved_size = _purge_by_sample(files, dry_run, int(fsize)) + saved_size
LOG.info("Will save approximately {:.1f}G space".format(saved_size / 1e9))
def setup_sample(f, analysis, amplicon=False, genome_build="hg19", **kw):
"""Setup config files, making backups and writing new files
:param path: root path in which to search for samples
:param dry_run: dry run flag
"""
if not os.path.exists(f):
return
with open(f) as fh:
config = yaml.load(fh)
## Check for correctly formatted config
if not config.get("details", None):
LOG.warn(
"Couldn't find 'details' section in config file {}: aborting setup!"
.format(f))
return
## Save file to backup if backup doesn't exist
f_bak = f.replace("-bcbb-config.yaml", "-bcbb-config.yaml.bak")
if not os.path.exists(f_bak):
LOG.info("Making backup of {} in {}".format(f, f_bak))
dry_backup(os.path.abspath(f), dry_run=kw['dry_run'])
## Save command file to backup if it doesn't exist
cmdf = f.replace("-bcbb-config.yaml", "-bcbb-command.txt")
if os.path.exists(cmdf):
cmdf_bak = cmdf.replace("-bcbb-command.txt", "-bcbb-command.txt.bak")
if not os.path.exists(cmdf_bak):
LOG.info("Making backup of {} in {}".format(cmdf, cmdf_bak))
dry_backup(os.path.abspath(cmdf), dry_run=kw['dry_run'])
## Save post_process file to backup if it doesn't exist
ppf = f.replace("-bcbb-config.yaml", "-post_process.yaml")
if os.path.exists(ppf):
ppf_bak = ppf.replace("-post_process.yaml", "-post_process.yaml.bak")
if not os.path.exists(ppf_bak):
LOG.info("Making backup of {} in {}".format(ppf, ppf_bak))
dry_backup(ppf, dry_run=kw['dry_run'])
if analysis:
config = update_sample_config(config, "analysis", analysis)
if genome_build:
config = update_sample_config(config, "genome_build", genome_build)
config = sort_sample_config_fastq(config)
## Remove config file and rewrite
dry_unlink(f, kw['dry_run'])
dry_write(f,
yaml.safe_dump(config,
default_flow_style=False,
allow_unicode=True,
width=1000),
dry_run=kw['dry_run'])
## Setup post process only if not provided at command line
if not kw.get("post_process", None):
ppfile = f.replace("-bcbb-config.yaml", "-post_process.yaml")
with open(ppfile) as fh:
pp = yaml.load(fh)
## Need to set working directory to path of bcbb-config.yaml file
if pp.get('distributed', {}).get('platform_args', None):
platform_args = pp['distributed']['platform_args'].split()
if "-D" in platform_args:
platform_args[platform_args.index("-D") +
1] = os.path.dirname(f)
elif "--workdir" in platform_args:
platform_args[platform_args.index("--workdir") +
1] = os.path.dirname(f)
pp['distributed']['platform_args'] = " ".join(platform_args)
## Change keys for all analyses
for anl in pp.get('custom_algorithms', {}).keys():
if kw.get('baits', None):
pp['custom_algorithms'][anl]['hybrid_bait'] = kw['baits']
if kw.get('targets', None):
pp['custom_algorithms'][anl]['hybrid_target'] = kw['targets']
if amplicon:
pp['custom_algorithms'][anl]['mark_duplicates'] = False
if amplicon:
LOG.info("setting amplicon analysis")
pp['algorithm']['mark_duplicates'] = False
if kw.get('galaxy_config', None):
pp['galaxy_config'] = kw['galaxy_config']
if kw.get('distributed', None):
LOG.info("setting distributed execution")
pp['algorithm']['num_cores'] = 'messaging'
elif kw.get('num_cores', None):
LOG.info("setting parallell execution")
pp['algorithm']['num_cores'] = kw['num_cores']
if kw.get('snpEff', None):
LOG.info("setting snpEff to {}".format(kw["snpEff"]))
pp['program']['snpEff'] = kw['snpEff']
dry_unlink(ppfile, dry_run=kw['dry_run'])
dry_write(ppfile,
yaml.safe_dump(pp,
default_flow_style=False,
allow_unicode=True,
width=1000),
dry_run=kw['dry_run'])