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Add task dl_and_run; rename ena options
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Original file line number | Diff line number | Diff line change |
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@@ -1,4 +1,5 @@ | ||
__all__ = [ | ||
"dl_and_run", | ||
"run_one_sample", | ||
"sim_schemes", | ||
] | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,53 @@ | ||
import logging | ||
import os | ||
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from viridian import tasks, utils | ||
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def viridian_finished(indir): | ||
try: | ||
log = utils.load_json(os.path.join(indir, "log.json.gz")) | ||
last_stage = log["run_summary"]["last_stage_completed"] | ||
except: | ||
return False | ||
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return last_stage == "Finished" | ||
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def run(options): | ||
with open(options.acc_file) as f: | ||
run_accessions = [x.rstrip() for x in f] | ||
logging.info(f"{len(run_accessions)} runs found in file {options.acc_file}") | ||
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if not os.path.exists(options.outdir): | ||
logging.info(f"Making main output directory {options.outdir}") | ||
os.mkdir(options.outdir) | ||
else: | ||
logging.info(f"Existing output directory found, using it: {options.outdir}") | ||
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options.keep_downloaded_reads = False | ||
options.reads1 = None | ||
options.reads2 = None | ||
options.reads = None | ||
options.reads_bam = None | ||
options.tech = None | ||
options.force = True | ||
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os.chdir(options.outdir) | ||
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for i, run in enumerate(run_accessions): | ||
message = f" STARTING {i+1}/{len(run_accessions)} {run} " | ||
logging.info(f"{message:#^60}") | ||
options.outdir = run | ||
options.run_accession = run | ||
options.sample_name = run | ||
if viridian_finished(options.outdir): | ||
logging.info(f"Already done, skipping: {run}") | ||
else: | ||
try: | ||
tasks.run_one_sample.run(options) | ||
except: | ||
logging.warn(f"Something went wrong: {run}") | ||
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message = f" FINISHED {run} " | ||
logging.info(f"{message:#^60}") |
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