def create_test_suite(module_names,
base_path,
overwrite=False,
printer=NullWriter()):
"""Creates a :py:class:`unittest.TestCase` for the ``main()`` method of
a command-line python module, and write these to modules
Parameters
----------
module_names : list
List of module names, as strings, to create :py:class:`~unittest.TestCase` s for
base_path : str
Path where test modules will be written
overwrite : bool, optional
If True, existing files will be overwritten (Default: False)
printer : file-like, optional
Logger to which output will be written
"""
for module_name in module_names:
printer.write(module_name)
short_name = get_short_name(module_name, separator="\.", terminator="")
output_str = TEST_TEMPLATE.replace("${MODULE}", module_name)
output_str = output_str.replace("${CAP_SHORT_NAME}",
short_name.capitalize())
output_str = output_str.replace("${SHORT_NAME}", short_name)
output_fn = os.path.join(base_path, "test_%s.py" % short_name)
if overwrite or not os.path.exists(output_fn):
printer.write("Writing %s" % output_fn)
fout = open(output_fn, "w")
fout.write(output_str)
fout.close()
def create_test_suite(module_names,base_path,overwrite=False,printer=NullWriter()):
"""Creates a :py:class:`unittest.TestCase` for the ``main()`` method of
a command-line python module, and write these to modules
Parameters
----------
module_names : list
List of module names, as strings, to create :py:class:`~unittest.TestCase` s for
base_path : str
Path where test modules will be written
overwrite : bool, optional
If True, existing files will be overwritten (Default: False)
printer : file-like, optional
Logger to which output will be written
"""
for module_name in module_names:
printer.write(module_name)
short_name = get_short_name(module_name,separator="\.",terminator="")
output_str = TEST_TEMPLATE.replace("${MODULE}",module_name)
output_str = output_str.replace("${CAP_SHORT_NAME}",short_name.capitalize())
output_str = output_str.replace("${SHORT_NAME}",short_name)
output_fn = os.path.join(base_path,"test_%s.py" % short_name)
if overwrite or not os.path.exists(output_fn):
printer.write("Writing %s" % output_fn)
fout = open(output_fn,"w")
fout.write(output_str)
fout.close()
def test_get_short_name():
tests = [("test", "test", {}), ("test.py", "test", dict(terminator=".py")),
("/home/jdoe/test.py", "test", dict(terminator=".py")),
("/home/jdoe/test.py.py", "test.py", dict(terminator=".py")),
("/home/jdoe/test.py.2", "test.py.2", {}),
("/home/jdoe/test.py.2", "test.py.2", dict(terminator=".py")),
("plastid.bin.test", "test", dict(separator="\.", terminator=""))]
for inp, expected, kwargs in tests:
found = get_short_name(inp, **kwargs)
msg = "test_get_short_name(): failed on input '%s'. Expected '%s'. Got '%s'" % (
inp, expected, found)
yield assert_equal, expected, found, msg
def get_short_samplename(inp):
"""Creates a sample legend label from a sample filename by removing everything including and after ``".txt"``
Parameters
----------
inp : str
filename
Returns
-------
str
"""
return get_short_name(inp, separator=os.path.sep, terminator=".txt")
def test_get_short_name():
tests = [("test","test",{}),
("test.py","test",dict(terminator=".py")),
("/home/jdoe/test.py","test",dict(terminator=".py")),
("/home/jdoe/test.py.py","test.py",dict(terminator=".py")),
("/home/jdoe/test.py.2","test.py.2",{}),
("/home/jdoe/test.py.2","test.py.2",dict(terminator=".py")),
("plastid.bin.test","test",dict(separator="\.",terminator=""))
]
for inp, expected, kwargs in tests:
found = get_short_name(inp,**kwargs)
msg = "test_get_short_name(): failed on input '%s'. Expected '%s'. Got '%s'" % (inp,expected,found)
yield assert_equal, expected, found, msg
import glob
import numpy as np
from plastid.genomics.genome_array import BAMGenomeArray
from plastid.util.io.openers import get_short_name
from plastid.util.io.filters import NameDateWriter
from plastid.util.scriptlib.help_formatters import format_module_docstring
from plastid.genomics.roitools import SegmentChain
from plastid.readers.bed import BED_Reader
# ignore and do not print any occurences of matching warnings
warnings.simplefilter("ignore")
# A stream to which stderr-like info can be written
# when printed in terminal, includes the script name, time & date
printer = NameDateWriter(get_short_name(inspect.stack()[-1][1]))
# create list of tuples [(SegmentChain, counts)]
def getCountVectorData(bedfile, bamList, bamIDs):
# read BED file to iterator of SegmentChain objects
bed_segmentChains = list(BED_Reader(open(bedfile)))
# create list of tuples (SegmentChain, [count_vectors/BAM])
countVectorData = []
# iterate through ROIs
for index, segment in enumerate(bed_segmentChains):
# prints in terminal progress every 100 ROIs processed
found in a `GFF3`_ file. Features with multiple parents are sorted into a category
called `Multiple`.
"""
from plastid.readers.gff import GFF3_Reader
from plastid.util.io.filters import NameDateWriter
from plastid.util.io.openers import get_short_name, opener, argsopener
from plastid.util.scriptlib.help_formatters import format_module_docstring
from plastid.util.scriptlib.argparsers import BaseParser
from collections import Counter
import argparse
import sys
import inspect
import warnings
warnings.simplefilter("once")
printer = NameDateWriter(get_short_name(inspect.stack()[-1][1]))
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
bp = BaseParser()