def report_summary(samples, run_parallel):
"""
Run coverage report with bcbiocov package
"""
work_dir = dd.get_work_dir(samples[0][0])
parent_dir = utils.safe_makedir(os.path.join(work_dir, "report"))
qsignature_fn = os.path.join(work_dir, "qc", "qsignature", "qsignature.ma")
with utils.chdir(parent_dir):
logger.info("copy qsignature")
if qsignature_fn:
if utils.file_exists(qsignature_fn) and not utils.file_exists("qsignature.ma"):
shutil.copy(qsignature_fn, "qsignature.ma")
out_dir = utils.safe_makedir("fastqc")
logger.info("summarize fastqc")
with utils.chdir(out_dir):
_merge_fastqc(samples)
out_dir = utils.safe_makedir("coverage")
out_dir = utils.safe_makedir("variants")
samples = run_parallel("coverage_report", samples)
try:
import bcbreport.prepare as bcbreport
bcbreport.report(parent_dir)
except:
logger.info("skipping report. No bcbreport installed.")
pass
logger.info("summarize metrics")
samples = _merge_metrics(samples)
return samples
def report_summary(samples, run_parallel):
"""
Run coverage report with bcbiocov package
"""
work_dir = dd.get_work_dir(samples[0][0])
parent_dir = utils.safe_makedir(os.path.join(work_dir, "report"))
qsignature_fn = os.path.join(work_dir, "qc", "qsignature", "qsignature.ma")
with utils.chdir(parent_dir):
logger.info("copy qsignature")
if qsignature_fn:
if utils.file_exists(qsignature_fn) and not utils.file_exists("qsignature.ma"):
shutil.copy(qsignature_fn, "qsignature.ma")
out_dir = utils.safe_makedir("fastqc")
logger.info("summarize fastqc")
with utils.chdir(out_dir):
_merge_fastqc(samples)
out_dir = utils.safe_makedir("coverage")
out_dir = utils.safe_makedir("variants")
samples = run_parallel("coverage_report", samples)
try:
import bcbreport.prepare as bcbreport
bcbreport.report(parent_dir)
except:
logger.info("skipping report. No bcbreport installed.")
pass
logger.info("summarize metrics")
samples = _merge_metrics(samples)
return samples
def _report_summary(samples, out_dir):
"""
Run coverage report with bcbiocov package
"""
try:
import bcbreport.prepare as bcbreport
except ImportError:
logger.info("skipping report. No bcbreport installed.")
return samples
# samples = utils.unpack_worlds(samples)
work_dir = dd.get_work_dir(samples[0])
parent_dir = utils.safe_makedir(out_dir)
with utils.chdir(parent_dir):
logger.info("copy qsignature")
qsignature_fn = os.path.join(work_dir, "qc", "qsignature",
"qsignature.ma")
if qsignature_fn: # this need to be inside summary/qc dict
if utils.file_exists(
qsignature_fn) and not utils.file_exists("qsignature.ma"):
shutil.copy(qsignature_fn, "bcbio_qsignature.ma")
out_dir = utils.safe_makedir("fastqc")
logger.info("summarize fastqc")
with utils.chdir(out_dir):
_merge_fastqc(samples)
logger.info("summarize metrics")
samples = _merge_metrics(samples)
logger.info("summarize target information")
samples = _merge_target_information(samples)
out_dir = utils.safe_makedir("coverage")
logger.info("summarize coverage")
for data in samples:
pfiles = tz.get_in(["summary", "qc", "coverage"], data, [])
if isinstance(pfiles, dict):
pfiles = [pfiles["base"]] + pfiles["secondary"]
elif pfiles:
pfiles = [pfiles]
for fn in pfiles:
if os.path.basename(fn).find("coverage_fixed") > -1:
utils.copy_plus(
fn, os.path.join(out_dir, os.path.basename(fn)))
out_dir = utils.safe_makedir("variants")
logger.info("summarize variants")
for data in samples:
pfiles = tz.get_in(["summary", "qc", "variants"], data, [])
if isinstance(pfiles, dict):
pfiles = [pfiles["base"]] + pfiles["secondary"]
elif pfiles:
pfiles = [pfiles]
for fn in pfiles:
if os.path.basename(fn).find("gc-depth-parse.tsv") > -1:
utils.copy_plus(
fn, os.path.join(out_dir, os.path.basename(fn)))
bcbreport.report(parent_dir)
out_report = os.path.join(parent_dir, "qc-coverage-report.html")
if not utils.file_exists(out_report):
rmd_file = os.path.join(parent_dir, "report-ready.Rmd")
run_file = "%s-run.R" % (os.path.splitext(out_report)[0])
with open(run_file, "w") as out_handle:
out_handle.write("""library(rmarkdown)\nrender("%s")\n""" %
rmd_file)
cmd = "%s %s" % (utils.Rscript_cmd(), run_file)
# Skip automated generation of coverage report to avoid error
# messages. We need to generalize coverage reporting and re-include.
# try:
# do.run(cmd, "Prepare coverage summary", log_error=False)
# except subprocess.CalledProcessError as msg:
# logger.info("Skipping generation of coverage report: %s" % (str(msg)))
if utils.file_exists("report-ready.html"):
shutil.move("report-ready.html", out_report)
return samples
def _report_summary(samples, out_dir):
"""
Run coverage report with bcbiocov package
"""
try:
import bcbreport.prepare as bcbreport
except ImportError:
logger.info("skipping report. No bcbreport installed.")
return samples
# samples = utils.unpack_worlds(samples)
work_dir = dd.get_work_dir(samples[0])
parent_dir = utils.safe_makedir(out_dir)
with utils.chdir(parent_dir):
logger.info("copy qsignature")
qsignature_fn = os.path.join(work_dir, "qc", "qsignature", "qsignature.ma")
if qsignature_fn: # this need to be inside summary/qc dict
if utils.file_exists(qsignature_fn) and not utils.file_exists("qsignature.ma"):
shutil.copy(qsignature_fn, "bcbio_qsignature.ma")
out_dir = utils.safe_makedir("fastqc")
logger.info("summarize fastqc")
with utils.chdir(out_dir):
_merge_fastqc(samples)
logger.info("summarize metrics")
samples = _merge_metrics(samples)
out_dir = utils.safe_makedir("coverage")
logger.info("summarize coverage")
for data in samples:
pfiles = tz.get_in(["summary", "qc", "coverage"], data, [])
if isinstance(pfiles, dict):
pfiles = [pfiles["base"]] + pfiles["secondary"]
elif pfiles:
pfiles = [pfiles]
for fn in pfiles:
if os.path.basename(fn).find("coverage_fixed") > -1:
utils.copy_plus(fn, os.path.join(out_dir, os.path.basename(fn)))
out_dir = utils.safe_makedir("variants")
logger.info("summarize variants")
for data in samples:
pfiles = tz.get_in(["summary", "qc", "variants"], data, [])
if isinstance(pfiles, dict):
pfiles = [pfiles["base"]] + pfiles["secondary"]
elif pfiles:
pfiles = [pfiles]
for fn in pfiles:
if os.path.basename(fn).find("gc-depth-parse.tsv") > -1:
utils.copy_plus(fn, os.path.join(out_dir, os.path.basename(fn)))
bcbreport.report(parent_dir)
out_report = os.path.join(parent_dir, "qc-coverage-report.html")
if not utils.file_exists(out_report):
rmd_file = os.path.join(parent_dir, "report-ready.Rmd")
run_file = "%s-run.R" % (os.path.splitext(out_report)[0])
with open(run_file, "w") as out_handle:
out_handle.write("""library(rmarkdown)\nrender("%s")\n""" % rmd_file)
cmd = "%s %s" % (utils.Rscript_cmd(), run_file)
# Skip automated generation of coverage report to avoid error
# messages. We need to generalize coverage reporting and re-include.
# try:
# do.run(cmd, "Prepare coverage summary", log_error=False)
# except subprocess.CalledProcessError, msg:
# logger.info("Skipping generation of coverage report: %s" % (str(msg)))
if utils.file_exists("report-ready.html"):
shutil.move("report-ready.html", out_report)
return samples
