def produce_report(genome_length, raw_reads, raw_mean, raw_n50, raw_p95,
raw_esize, raw_bases, raw_coverage, length_cutoff,
seed_reads, seed_bases, seed_mean, seed_n50, seed_p95,
seed_esize, seed_coverage, preassembled_reads,
preassembled_mean, preassembled_n50, preassembled_p95,
preassembled_esize, preassembled_bases,
preassembled_coverage, preassembled_yield,
preassembled_seed_fragmentation,
preassembled_seed_truncation, **ignored):
"""Return a preassembly report as JSON string.
Parameters are as defined in the spec-file.
Extra parameters are ignored, so that the caller may be
augmented in a separate commit prior to updates here.
(That facilitates cross-team collaboration.)
"""
log.info("Starting {f!r}".format(f=os.path.basename(__file__)))
# Report Attributes
attrs = []
attrs.append(Attribute('genome_length', genome_length))
attrs.append(Attribute('raw_reads', raw_reads))
attrs.append(Attribute('raw_mean', int(round(raw_mean))))
attrs.append(Attribute('raw_n50', raw_n50))
attrs.append(Attribute('raw_p95', raw_p95))
attrs.append(Attribute('raw_esize', raw_esize))
attrs.append(Attribute('raw_bases', raw_bases))
attrs.append(Attribute('raw_coverage', raw_coverage))
attrs.append(Attribute('length_cutoff', length_cutoff))
attrs.append(Attribute('seed_reads', seed_reads))
attrs.append(Attribute('seed_mean', int(round(seed_mean))))
attrs.append(Attribute('seed_n50', seed_n50))
attrs.append(Attribute('seed_p95', seed_p95))
attrs.append(Attribute('seed_esize', seed_esize))
attrs.append(Attribute('seed_bases', seed_bases))
attrs.append(Attribute('seed_coverage', seed_coverage))
attrs.append(Attribute('preassembled_reads', preassembled_reads))
attrs.append(Attribute('preassembled_mean', int(round(preassembled_mean))))
attrs.append(Attribute('preassembled_n50', preassembled_n50))
attrs.append(Attribute('preassembled_p95', preassembled_p95))
attrs.append(Attribute('preassembled_esize', preassembled_esize))
attrs.append(Attribute('preassembled_bases', preassembled_bases))
attrs.append(
Attribute('preassembled_coverage', int(round(preassembled_coverage))))
attrs.append(Attribute('preassembled_yield', preassembled_yield))
attrs.append(
Attribute('preassembled_seed_fragmentation',
preassembled_seed_fragmentation))
attrs.append(
Attribute('preassembled_seed_truncation',
preassembled_seed_truncation))
report = Report(Constants.R_ID, title='Preassembly', attributes=attrs)
from pbreports.io.specs import load_spec
spec = load_spec(Constants.R_ID)
report = spec.apply_view(report)
return report.to_json()
def produce_report(
genome_length,
raw_reads,
raw_mean,
raw_n50,
raw_p95,
raw_bases,
raw_coverage,
length_cutoff,
seed_reads,
seed_bases,
seed_mean,
seed_n50,
seed_p95,
seed_coverage,
preassembled_reads,
preassembled_mean,
preassembled_n50,
preassembled_p95,
preassembled_bases,
preassembled_coverage,
preassembled_yield,
preassembled_seed_fragmentation,
preassembled_seed_truncation,
**ignored
):
"""Return a preassembly report as JSON string.
Parameters are as defined in the spec-file.
Extra parameters are ignored, so that the caller may be
augmented in a separate commit prior to updates here.
(That facilitates cross-team collaboration.)
"""
log.info("Starting {f!r}".format(
f=os.path.basename(__file__)))
# Report Attributes
attrs = []
attrs.append(Attribute('genome_length', genome_length))
attrs.append(Attribute('raw_reads', raw_reads))
attrs.append(Attribute('raw_mean', int(round(raw_mean))))
attrs.append(Attribute('raw_n50', raw_n50))
attrs.append(Attribute('raw_p95', raw_p95))
attrs.append(Attribute('raw_bases', raw_bases))
attrs.append(Attribute('raw_coverage', raw_coverage))
attrs.append(Attribute('length_cutoff', length_cutoff))
attrs.append(Attribute('seed_reads', seed_reads))
attrs.append(Attribute('seed_mean', int(round(seed_mean))))
attrs.append(Attribute('seed_n50', seed_n50))
attrs.append(Attribute('seed_p95', seed_p95))
attrs.append(Attribute('seed_bases', seed_bases))
attrs.append(Attribute('seed_coverage', seed_coverage))
attrs.append(Attribute('preassembled_reads', preassembled_reads))
attrs.append(Attribute('preassembled_mean', int(round(preassembled_mean))))
attrs.append(Attribute('preassembled_n50', preassembled_n50))
attrs.append(Attribute('preassembled_p95', preassembled_p95))
attrs.append(Attribute('preassembled_bases', preassembled_bases))
attrs.append(Attribute('preassembled_coverage', int(round(preassembled_coverage))))
attrs.append(Attribute('preassembled_yield', preassembled_yield))
attrs.append(Attribute('preassembled_seed_fragmentation', preassembled_seed_fragmentation))
attrs.append(Attribute('preassembled_seed_truncation', preassembled_seed_truncation))
report = Report(Constants.R_ID, title='Preassembly', attributes=attrs)
from pbreports.io.specs import load_spec
spec = load_spec(Constants.R_ID)
report = spec.apply_view(report)
return report.to_json()
def produce_report(
genome_length,
raw_reads,
raw_mean,
raw_n50,
raw_p95,
raw_bases,
raw_coverage,
length_cutoff,
seed_reads,
seed_bases,
seed_mean,
seed_n50,
seed_p95,
seed_coverage,
preassembled_reads,
preassembled_mean,
preassembled_n50,
preassembled_p95,
preassembled_bases,
preassembled_coverage,
preassembled_yield,
preassembled_seed_fragmentation,
preassembled_seed_truncation,
**ignored
):
"""Return a preassembly report as JSON string.
Parameters are as defined in the spec-file.
Extra parameters are ignored, so that the caller may be
augmented in a separate commit prior to updates here.
(That facilitates cross-team collaboration.)
"""
log.info("Starting {f!r}".format(
f=os.path.basename(__file__)))
# Report Attributes
attrs = []
attrs.append(Attribute('genome_length', genome_length,
name="Genome Length (user input)"))
attrs.append(Attribute('raw_reads', raw_reads, name="Number of Raw Reads"))
attrs.append(Attribute('raw_mean', int(
round(raw_mean)), name="Raw Read Length Mean"))
attrs.append(Attribute('raw_n50', raw_n50, name="Raw Read Length (N50)"))
attrs.append(Attribute('raw_p95', raw_p95, name="Raw Read Length 95%"))
attrs.append(Attribute('raw_bases', raw_bases,
name="Number of Raw Bases (total)"))
attrs.append(Attribute('raw_coverage', raw_coverage,
name="Raw Coverage (bases/genome_size)"))
attrs.append(Attribute('length_cutoff', length_cutoff,
name="Length Cutoff (user input or auto-calc)"))
attrs.append(Attribute('seed_reads', seed_reads,
name="Number of Seed Reads"))
attrs.append(Attribute('seed_mean', int(
round(seed_mean)), name="Seed Read Length Mean"))
attrs.append(Attribute('seed_n50', seed_n50,
name="Seed Read Length (N50)"))
attrs.append(Attribute('seed_p95', seed_p95, name="Seed Read Length 95%"))
attrs.append(Attribute('seed_bases', seed_bases,
name="Number of Seed Bases (total)"))
attrs.append(Attribute('seed_coverage', seed_coverage,
name="Seed Coverage (bases/genome_size)"))
attrs.append(Attribute('preassembled_reads', preassembled_reads,
name="Number of Pre-Assembled Reads"))
attrs.append(Attribute('preassembled_mean', int(
round(preassembled_mean)), name="Pre-Assembled Read Length Mean"))
attrs.append(Attribute('preassembled_n50', preassembled_n50,
name="Pre-Assembled Read Length (N50)"))
attrs.append(Attribute('preassembled_p95', preassembled_p95,
name="Pre-Assembled Read Length 95%"))
attrs.append(Attribute('preassembled_bases', preassembled_bases,
name="Number of Pre-Assembled Bases (total)"))
attrs.append(Attribute('preassembled_coverage', int(round(
preassembled_coverage)), name="Pre-Assembled Coverage (bases/genome_size)"))
attrs.append(Attribute('preassembled_yield', preassembled_yield,
name="Pre-Assembled Yield (bases/seed_bases)"))
attrs.append(Attribute('preassembled_seed_fragmentation', preassembled_seed_fragmentation,
name="Avg number of reads that each seed is broken into."))
attrs.append(Attribute('preassembled_seed_truncation',
preassembled_seed_truncation, name="Avg number of bases lost from each seed."))
report = Report(Constants.R_ID, title='Preassembly', attributes=attrs)
from pbreports.io.specs import load_spec
spec = load_spec(Constants.R_ID)
report = spec.apply_view(report)
return report.to_json()
class HgapCoverageReport(coverage_base.CoverageReport):
TOOL_ID = "pbreports.tasks.coverage_report_hgap"
DRIVER_EXE = "python -m pbreports.report.coverage_hgap --resolved-tool-contract "
spec = load_spec("coverage_hgap")