def setUp(self):
self.db = CoreDb(":memory:")
self.db.create_tables()
self.run_args = [
"abc",
"--lane",
"1",
"--date",
"2008-09-21",
"--type",
"Illumina-MiSeq",
"--comment",
"mdsnfa adsf",
]
self.samples = [{
"SampleID": "abc123",
"BarcodeSequence": "GGGCCT",
"SampleType": "Oral swab",
"bb": "cd e29",
}]
def setUp(self):
self.db = CoreDb(":memory:")
self.db.create_tables()
self.run = (
u"2015-10-11",
u"HiSeq",
u"Nextera XT",
1,
u"run_file.fastq",
u"Bob's run",
)
self.run_acc = self.db.register_run(*self.run)
self.sample_bcs = [
("Sample1", "ABC"),
("Sample2", "DEF"),
("My.Sample3", "GHI"),
]
self.single_sample = self.sample_bcs[0]
self.annotations = {
"SampleType": "Oral swab",
"SubjectID": "Subj23",
"study_group": "Healthy",
"study_day": "1",
}
"""Add samples and runs to the registry"""
import argparse
import itertools
import os
import re
import sys
import gzip
from sample_registry.db import CoreDb
from sample_registry.mapping import SampleTable
from sample_registry.illumina import IlluminaFastq
REGISTRY_DATABASE = CoreDb("/var/local/sample_registry/core.db")
SAMPLES_DESC = """\
Add new samples to the registry, with annotations.
"""
ANNOTATIONS_DESC = """\
Replace annotations for samples in the registry. Samples are matched
using the sample ID and barcode sequence.
"""
ANNOTATIONS_EPILOG = """\
**BEWARE USER** This script will replace all existing annotations with
those found in the provided file! Make sure this is what you want, or
you will be restoring database tables from backup files, as you deserve.
You have been warned!!!
"""
