def setUpClass(cls):
"""
Load data once.
"""
try:
if cls.DATA_DIR is not None:
log.info('data has already been loaded')
return
cls.DATA_DIR = os.path.join(_get_root_data_dir(), 'control')
cmph5 = os.path.join(cls.DATA_DIR, 'control_reads.cmp.h5')
csv = os.path.join(cls.DATA_DIR, 'filtered_summary.csv')
log.info('Loading data 1 time from {c} and {f}'.format(
c=cmph5, f=csv))
cls._data = {}
cls._data[CONTROL_READS] = _get_control_reads(cmph5)
cls._data[FILTERED_READS] = _get_filtered_reads(csv)
except:
tb = traceback.format_exc()
log.error(tb)
print(tb)
raise
class TestTopVariantsReportEcoli(TestTopVariantsReport):
CONTIG_ID = "ecoliK12_pbi_March2013"
DATA_DIR = op.join(_get_root_data_dir(), "topvariants")
REFERENCE = "/pbi/dept/secondary/siv/references/ecoliK12_pbi_March2013/sequence/ecoliK12_pbi_March2013.fasta"
VARIANTS_GFF = op.join(DATA_DIR, "variants.gff.gz")
RARE_VARIANTS_GFF = op.join(DATA_DIR, "rare_variants.gff.gz")
N_TOP_VARIANTS = 9
TABLE_ROW_FIRST = [
CONTIG_ID,
1849183L,
'1849183_1849184insT',
'INS',
20,
48,
'haploid',
]
TABLE_ROW_LAST = [
CONTIG_ID,
3785544L,
'3785544_3785545insA',
'INS',
18,
40,
'haploid',
]
def setUpClass(cls):
"""
Load data once.
"""
try:
if cls.DATA_DIR is not None:
log.info('data has already been loaded')
return
cls.DATA_DIR = os.path.join(_get_root_data_dir(), 'control')
cmph5 = os.path.join(cls.DATA_DIR, 'control_reads.cmp.h5')
csv = os.path.join(cls.DATA_DIR, 'filtered_summary.csv')
log.info('Loading data 1 time from {c} and {f}'.format(c=cmph5,
f=csv))
cls._data = {}
cls._data[CONTROL_READS] = _get_control_reads(cmph5)
cls._data[FILTERED_READS] = _get_filtered_reads(csv)
except:
tb = traceback.format_exc()
log.error(tb)
print(tb)
raise
from pbcore.io import ReferenceSet
import pbcore.data
from pbreports.util import openReference
from pbreports.util import get_top_contigs_from_ref_entry
from pbreports.report.variants import (make_variants_report, _extract_alignment_summ_data,
LENGTH, GAPS, ERR, COV,
_append_variants_gff_data,
_get_consensus_table_and_attributes,
_ref_ids_ordered_by_len,
_create_variants_plot_grp, _create_bars, _get_legend_file)
from base_test_case import _get_root_data_dir, run_backticks, \
skip_if_data_dir_not_present, LOCAL_DATA
VARIANTS_DATA = op.join(_get_root_data_dir(), 'variants')
DT='Desulfurobacterium_thermolithotrophum_DSM11699_gDNA'
log = logging.getLogger(__name__)
class BaseTestCase(object):
def setUp(self):
"""
Before *every* test
"""
self._output_dir = tempfile.mkdtemp(suffix="variants")
def tearDown(self):
"""
Tests for end-to-end tool contract support. Any report tool that has emit and
resolve functions should have a class here.
"""
import unittest
import os.path
import pbcommand.testkit
from base_test_case import _get_root_data_dir
ROOT_DIR = _get_root_data_dir()
READ_FAS = os.path.join(ROOT_DIR, 'preassembly',
'filtered_subreads.fasta')
LONG_FAS = os.path.join(ROOT_DIR, 'preassembly',
'filtered_longreads.fasta')
CORR_FAS = os.path.join(ROOT_DIR, 'preassembly',
'corrected.fasta')
LEN_CUT = 6000
@unittest.skipUnless(os.path.isdir(ROOT_DIR), "%s not available" % ROOT_DIR)
class TestPolishedAssembly(pbcommand.testkit.PbTestApp):
DRIVER_BASE = "python -m pbreports.report.preassembly "
DRIVER_EMIT = DRIVER_BASE + " --emit-tool-contract "
DRIVER_RESOLVE = DRIVER_BASE + " --resolved-tool-contract "
REQUIRES_PBCORE = True
INPUT_FILES = [
READ_FAS,
def setUp(self):
"""
Before *every* test
"""
self._data_dir = os.path.join(_get_root_data_dir(), 'coverage')
self._output_dir = tempfile.mkdtemp(suffix="coverage")
from pbcore.io import ReferenceSet
import pbtestdata
from pbreports.util import openReference
from pbreports.util import get_top_contigs_from_ref_entry
from pbreports.report.variants import (
make_variants_report, _extract_alignment_summ_data, LENGTH, GAPS, ERR, COV,
_append_variants_gff_data, _get_consensus_table_and_attributes,
_ref_ids_ordered_by_len, _create_variants_plot_grp, _create_bars,
_get_legend_file)
from base_test_case import _get_root_data_dir, run_backticks, \
skip_if_data_dir_not_present, LOCAL_DATA
VARIANTS_DATA = op.join(_get_root_data_dir(), 'variants')
DT = 'Desulfurobacterium_thermolithotrophum_DSM11699_gDNA'
log = logging.getLogger(__name__)
class BaseTestCase(object):
def setUp(self):
"""
Before *every* test
"""
self._output_dir = tempfile.mkdtemp(suffix="variants")
def tearDown(self):
"""
