def inner():
inner_reader, inner_writer = get_pipes()
wrapped = catch_stderr(inner_writer)(stderr_func)
# make sure value is returned from wrapped function
msg = wrapped(message)
assert_equal(message, msg)
# make sure we caught entire message from stderr
inner_writer.flush()
inner_writer.close()
assert_equal(message, inner_reader.read())
inner_reader.close()
def inner():
inner_reader, inner_writer = get_pipes()
wrapped = catch_stderr(inner_writer)(stderr_func)
# make sure value is returned from wrapped function
msg = wrapped(message)
assert_equal(message,msg)
# make sure we caught entire message from stderr
inner_writer.flush()
inner_writer.close()
assert_equal(message,inner_reader.read())
inner_reader.close()
from pkg_resources import resource_filename, cleanup_resources
from plastid.test.functional.base import execute_helper
from plastid.test.ref_files import RPATH, REF_FILES, \
COUNT_OPTIONS, \
ANNOTATION_OPTIONS, \
MASK_OPTIONS
from plastid.genomics.genome_array import GenomeArray
from plastid.bin.make_wiggle import main
from plastid.util.services.decorators import catch_stderr
#===============================================================================
# INDEX: global constants used by tests
#===============================================================================
test_info = {
"test_method" : catch_stderr()(main),
"module_name" : "plastid.bin.make_wiggle",
"ref_file_path" : resource_filename("plastid","test/data/command_line"),
"temp_file_path" : tempfile.mkdtemp(prefix="make_wiggle"),
}
"""Constants used in tests below"""
#===============================================================================
# INDEX: programmatically define tests
#===============================================================================
# Define tests as tuples of:
# 1. Command-line style arguments to pass to ``main``
# 2. A list of reference files that output should be compared against
# 3. A list of output files created by running ``main`` with the arguments provided in (1)
# 4. A list of strings specifying how equality should be evaluated
from pkg_resources import resource_filename, cleanup_resources
from plastid.test.functional.base import execute_helper
from plastid.test.ref_files import COUNT_OPTIONS, \
ANNOTATION_OPTIONS, \
MASK_OPTIONS
from plastid.bin.cs import main
from plastid.util.services.decorators import catch_stderr
#===============================================================================
# INDEX: global constants used by tests
#===============================================================================
test_info = {
"test_method" : catch_stderr()(main),
"module_name" : "plastid.bin.cs",
"ref_file_path" : resource_filename("plastid","test/data/command_line"),
"temp_file_path" : tempfile.mkdtemp(prefix="cs"),
}
"""Constants used by multiple tests"""
_outbase = os.path.join(test_info["temp_file_path"],"test_cs")
_file_stubs = [
'merged.txt',
'gene.positions',
'transcript.positions',
'gene_cds.bed',
'gene_exon.bed',
'gene_masked.bed',
import sys
import shlex
import shutil
import inspect
import os
import nose
from nose.tools import assert_true
from plastid.util.io.filters import NameDateWriter
from plastid.util.io.openers import get_short_name, NullWriter
from plastid.bin.test_table_equality import main
from plastid.util.services.decorators import skip_if_abstract, catch_stderr
from pkg_resources import resource_filename, cleanup_resources
printer = NameDateWriter(get_short_name(inspect.stack()[-1][1]))
table_test = catch_stderr()(main)
#===============================================================================
# INDEX: test generator functions
#===============================================================================
def check_one_file(test_info, ref_file, output_file, eq_args):
"""Check a single output file produced by a test run against a reference file
Parameters
----------
test_info : dict
Dictionary containing miscellaneous test information
ref_file : str
import sys
import shlex
import shutil
import inspect
import os
import nose
from nose.tools import assert_true
from plastid.util.io.filters import NameDateWriter
from plastid.util.io.openers import get_short_name, NullWriter
from plastid.bin.test_table_equality import main
from plastid.util.services.decorators import skip_if_abstract, catch_stderr
from pkg_resources import resource_filename, cleanup_resources
printer = NameDateWriter(get_short_name(inspect.stack()[-1][1]))
table_test = catch_stderr()(main)
#===============================================================================
# INDEX: test generator functions
#===============================================================================
def check_one_file(test_info,ref_file,output_file,eq_args):
"""Check a single output file produced by a test run against a reference file
Parameters
----------
test_info : dict
Dictionary containing miscellaneous test information
ref_file : str
Name of reference file, excluding path, against which test output will be checked
from tempfile import NamedTemporaryFile
from pkg_resources import cleanup_resources
from nose.plugins.attrib import attr
from nose.tools import assert_equal
from plastid.util.io.filters import CommentWriter
from plastid.util.io.openers import NullWriter
from plastid.genomics.roitools import GenomicSegment
from plastid.bin.test_table_equality import main
from plastid.util.services.decorators import catch_stderr
size = 5000
#capture output
run_main = catch_stderr()(main)
@attr(test="functional")
def test_exit_status():
# define columns
cols = {
"intA" : numpy.random.randint(0,high=2**16,size=size),
"intB" : numpy.random.randint(-10,high=20,size=size),
"idxA" : numpy.arange(size),
"chrA" : numpy.array([chr(65+(X%(91-65))) for X in range(size)]),
"strA" : numpy.array([str(GenomicSegment("chrA",X,X+500,"+")) for X in range(size)]),
"strB" : numpy.array([str(GenomicSegment("chrB",X/2,X/2+500,"-")) for X in range(size)]),
"floatA" : 10*numpy.random.randn(size) + 500,
"floatB" : (10**-5)*numpy.random.random(size),
"objA" : numpy.tile(None,5000),
def inner():
# make sure value is returned from wrapped function
wrapped = catch_stderr()(stderr_func)
msg = wrapped(message)
assert_equal(msg, message)
from plastid.test.functional.base import execute_helper
from plastid.test.ref_files import RPATH, REF_FILES, \
COUNT_OPTIONS, \
ANNOTATION_OPTIONS, \
MASK_OPTIONS
from plastid.bin.get_count_vectors import main
from plastid.util.services.decorators import catch_stderr
from plastid.util.services.mini2to3 import cStringIO
#===============================================================================
# INDEX: global constants used by tests
#===============================================================================
get_count_vectors_test_info = {
"test_method":
catch_stderr()(main),
"module_name":
"plastid.bin.get_count_vectors",
"ref_file_path":
resource_filename("plastid", "test/data/command_line/gen_count_vectors"),
"temp_file_path":
tempfile.mkdtemp(prefix="get_count_vectors"),
}
# Define tests as tuples of:
# 1. Command-line style arguments to pass to ``main``
# 2. A list of reference files that output should be compared against
# 3. A list of output files created by running ``main`` with the arguments provided in (1)
# 4. A list of strings specifying how equality should be evaluated
ref_files = []
out_files = []
def inner():
# make sure value is returned from wrapped function
wrapped = catch_stderr()(stderr_func)
msg = wrapped(message)
assert_equal(msg,message)
from pkg_resources import resource_filename, cleanup_resources
from nose.plugins.attrib import attr
from plastid.test.functional.base import execute_helper
from plastid.test.ref_files import RPATH, REF_FILES, \
COUNT_OPTIONS, \
ANNOTATION_OPTIONS, \
MASK_OPTIONS
from plastid.bin.test_table_equality import main as table_test
from plastid.bin.metagene import main
from plastid.util.services.decorators import catch_stderr
#===============================================================================
# INDEX: global constants used by tests
#===============================================================================
TEST_INFO = { "test_method" : catch_stderr()(main),
"module_name" : "plastid.bin.metagene",
"ref_file_path" : resource_filename("plastid","test/data/command_line"),
"temp_file_path" : tempfile.mkdtemp(prefix="metagene"),
}
_basename = os.path.join(TEST_INFO["temp_file_path"],"test_metagene")
#===============================================================================
# INDEX: tests
#===============================================================================
tests = [
# test generate cds start
(
"generate %s_cds_start --downstream 100 %s %s" % (_basename, ANNOTATION_OPTIONS, MASK_OPTIONS),