def test_main_versionOption(self):
with patch('sys.stdout', new=StringIO()) as mockStdout:
sys.argv = ['sort', '--version']
sort.main()
self.assertTrue(
-1 != mockStdout.getvalue().find('Written by Aldebaran Perseke'))
def test_main_stdin_dictionaryOrder(self):
with patch('sys.stdout', new=StringIO()) as mockStdout:
with patch('sys.stdin',
new=StringIO('+ghi\nab-c\ndef)\n[jkl')) as mockStdin:
sys.argv = ['sort', '--dictionary-order']
sort.main()
self.assertTrue('ab-c\ndef)\n+ghi\n[jkl\n' == mockStdout.getvalue())
def test_main_stdin_reverse(self):
with patch('sys.stdout', new=StringIO()) as mockStdout:
with patch('sys.stdin',
new=StringIO('def\nabc\njkl\nghi')) as mockStdin:
sys.argv = ['sort', '--reverse']
sort.main()
self.assertTrue('jkl\nghi\ndef\nabc\n' == mockStdout.getvalue())
def test_main_stdin_ignoreCase(self):
with patch('sys.stdout', new=StringIO()) as mockStdout:
with patch('sys.stdin',
new=StringIO('DEF\nabc\nJKL\nghi')) as mockStdin:
sys.argv = ['sort', '--ignore-case']
sort.main()
self.assertTrue('abc\nDEF\nghi\nJKL\n' == mockStdout.getvalue())
def test_main_invalidOption(self):
with patch('sys.stderr', new=StringIO()) as mockStderr:
with self.assertRaises(SystemExit) as exit:
sys.argv = ['sort', '-a', '--reverse']
sort.main()
self.assertEqual(exit.exception.code, 2)
self.assertTrue(
-1 != mockStderr.getvalue().find('unrecognized arguments: -a'))
def test_main_hifenAsFileNames(self):
with patch('sys.stdout', new=StringIO()) as mockStdout:
with patch(
'sys.stdin',
new=StringIO('def\njkl\nabc\nmno\nxyz\nghi')) as mockStdin:
sys.argv = ['sort', '-']
sort.main()
self.assertTrue(
'abc\ndef\nghi\njkl\nmno\nxyz\n' == mockStdout.getvalue())
def test_main_stdin_ignoreLeadingBlanks(self):
with patch('sys.stdout', new=StringIO()) as mockStdout:
with patch(
'sys.stdin',
new=StringIO(' def\n abc\n jkl\n ghi')) as mockStdin:
sys.argv = ['sort', '--ignore-leading-blanks']
sort.main()
self.assertTrue(
' abc\n def\n ghi\n jkl\n' == mockStdout.getvalue())
def test_main_singleFileName(self):
contentFile = tempfile.NamedTemporaryFile(delete=False)
contentFile.write(b'def\njkl\nabc\nmno\nxyz\nghi')
contentFile.close()
with patch('sys.stdout', new=StringIO()) as mockStdout:
sys.argv = ['sort', contentFile.name]
sort.main()
self.assertTrue(
'abc\ndef\nghi\njkl\nmno\nxyz\n' == mockStdout.getvalue())
os.remove(contentFile.name)
def test_main_invalidFileName(self):
# remember, a temporary file is removed after it's closed
invalidFile = tempfile.NamedTemporaryFile()
invalidFileName = invalidFile.name
invalidFile.write(b'abcdef\nghijklm\nnopqrs\ntuvwxyz')
invalidFile.close()
with patch('sys.stderr', new=StringIO()) as mockStderr:
sys.argv = ['sort', invalidFileName]
sort.main()
self.assertTrue(
-1 != mockStderr.getvalue().find('No such file or directory'))
def test_main_singleFileNameAndHifen(self):
contentFile = tempfile.NamedTemporaryFile(delete=False)
contentFile.write(b'stuvwxyz\nmnopqr\n')
contentFile.close()
with patch('sys.stdout', new=StringIO()) as mockStdout:
with patch('sys.stdin',
new=StringIO('abcdef\nghijkl\n')) as mockStdin:
sys.argv = ['sort', contentFile.name, '-']
sort.main()
self.assertTrue(
'abcdef\nghijkl\nmnopqr\nstuvwxyz\n' == mockStdout.getvalue())
os.remove(contentFile.name)
def test_sample(test):
n = []
times = []
for item in test:
item_counter, timing = sort.main(item)
n.append(item_counter)
times.append(timing)
return n, times
def callSort(sortFile, arguments=[]):
try:
if sortFile == 'sort.py':
sort.main(arguments)
elif sortFile == 'sortUrls.py':
print(arguments)
sortUrls.main(arguments)
else:
raise Exception('File sorting implementation not included/found.')
except IOError as e:
print "Error: File \"" + argv[1] + "\" not found."
except IndexError as e:
print errorMessage
except ValueError as e:
print errorMessage
except KeyError as e:
print errorMessage
def callSort(sortFile, arguments=[]):
try:
if sortFile == 'sort.py':
sort.main(arguments)
elif sortFile == 'sortUrls.py':
print(arguments)
sortUrls.main(arguments)
else:
raise Exception('File sorting implementation not included/found.')
except IOError as e:
print "Error: File \"" + argv[1] + "\" not found."
except IndexError as e:
print errorMessage
except ValueError as e:
print errorMessage
except KeyError as e:
print errorMessage
def test_main_multipleFileNames(self):
firstContentFile = tempfile.NamedTemporaryFile(delete=False)
firstContentFile.write(b'stuvwxyz\nmnopqr\n')
firstContentFile.close()
secondContentFile = tempfile.NamedTemporaryFile(delete=False)
secondContentFile.write(b'abcdef\nghijkl\n')
secondContentFile.close()
with patch('sys.stdout', new=StringIO()) as mockStdout:
sys.argv = ['sort', firstContentFile.name, secondContentFile.name]
sort.main()
self.assertTrue(
'abcdef\nghijkl\nmnopqr\nstuvwxyz\n' == mockStdout.getvalue())
os.remove(firstContentFile.name)
os.remove(secondContentFile.name)
def main():
usage = "Usage: vcfPytools.py [tool] [options]\n\n" + \
"Available tools:\n" + \
" annotate:\n\tAnnotate the vcf file with membership in other vcf files.\n" + \
" extract:\n\tExtract vcf records from a region.\n" + \
" filter:\n\tFilter the vcf file.\n" + \
" indel:\n\tIndel manipulation tools.\n" + \
" intersect:\n\tGenerate the intersection of two vcf files.\n" + \
" merge:\n\tMerge a list of vcf files.\n" + \
" multi:\n\tFind the intersections and unique fractions of multiple vcf files.\n" + \
" sort:\n\tSort a vcf file.\n" + \
" stats:\n\tGenerate statistics from a vcf file.\n" + \
" union:\n\tGenerate the union of two vcf files.\n" + \
" unique:\n\tGenerate the unique fraction from two vcf files.\n" + \
" validate:\n\tValidate the input vcf file.\n\n" + \
"vcfPytools.py [tool] --help for information on a specific tool."
# Determine the requested tool.
if len(sys.argv) > 1:
tool = sys.argv[1]
else:
print >> sys.stderr, usage
exit(1)
if tool == "annotate":
import annotate
success = annotate.main()
elif tool == "extract":
import extract
success = extract.main()
elif tool == "filter":
import filter
success = filter.main()
elif tool == "intersect":
import intersect
success = intersect.main()
elif tool == "indel":
import indel
success = indel.main()
elif tool == "multi":
import multi
success = multi.main()
elif tool == "merge":
import merge
success = merge.main()
elif tool == "sort":
import sort
success = sort.main()
elif tool == "stats":
import stats
success = stats.main()
elif tool == "union":
import union
success = union.main()
elif tool == "unique":
import unique
success = unique.main()
elif tool == "test":
import test
success = test.main()
elif tool == "validate":
import validate
success = validate.main()
elif tool == "--help" or tool == "-h" or tool == "?":
print >> sys.stderr, usage
else:
print >> sys.stderr, "Unknown tool: ", tool
print >> sys.stderr, "\n", usage
exit(1)
# If program completed properly, terminate.
if success == 0: exit(0)
# sleep(10)
print "this is child process end."
else: # 父进程
# sleep(60)
# 排序，生成榜单
print "this is parent process start."
ppid1 = os.fork()
if ppid1 == 0:
pppid2 = os.fork()
if pppid2 == 0:
print "this is child process. run zongheng"
cmdline.execute("scrapy crawl zongheng".split())
else:
import time
time.sleep(9)
print "this is child process. run chuangshi"
cmdline.execute("scrapy crawl chuangshi".split())
else:
ppppid3 = os.fork()
if ppppid3 == 0:
import time
time.sleep(6)
print "this is child process. run seventeen"
cmdline.execute("scrapy crawl seventeen".split())
else:
sleep(300)
st.main()
print "this is parent process. exe st()"
print "this is parent process end."
except OSError, e:
pass
import os
import sort
import pandas as pd
from pylatex.utils import italic, NoEscape
from pylatex.basic import NewLine
from pylatex.base_classes import Arguments
from pylatex import Document, Section, Itemize, Command, Package, Subsection
sort.main()
geometry_options = {'margin': '1in'}
document = Document('.', geometry_options=geometry_options)
document.packages.append(Package('hyperref'))
document.preamble.append(Command('title', 'Reading List'))
document.preamble.append(Command('author', 'Daniel Saunders'))
document.preamble.append(Command('date', NoEscape(r'\today')))
document.append(NoEscape(r'\maketitle'))
document.append('Note: Work in progress. Some dates before mid-July 2018 are approximate.')
def create_read_section(document, medium):
with document.create(Subsection('Read')):
with document.create(Itemize()) as itemize:
try:
df = pd.read_csv(os.path.join(medium, 'read.csv'))
except pd.errors.EmptyDataError:
def main():
usage = "Usage: vcfPytools.py [tool] [options]\n\n" + \
"Available tools:\n" + \
" annotate:\n\tAnnotate the vcf file with membership in other vcf files.\n" + \
" extract:\n\tExtract vcf records from a region.\n" + \
" filter:\n\tFilter the vcf file.\n" + \
" indel:\n\tIndel manipulation tools.\n" + \
" intersect:\n\tGenerate the intersection of two vcf files.\n" + \
" merge:\n\tMerge a list of vcf files.\n" + \
" multi:\n\tFind the intersections and unique fractions of multiple vcf files.\n" + \
" sort:\n\tSort a vcf file.\n" + \
" stats:\n\tGenerate statistics from a vcf file.\n" + \
" union:\n\tGenerate the union of two vcf files.\n" + \
" unique:\n\tGenerate the unique fraction from two vcf files.\n" + \
" validate:\n\tValidate the input vcf file.\n\n" + \
"vcfPytools.py [tool] --help for information on a specific tool."
# Determine the requested tool.
if len(sys.argv) > 1:
tool = sys.argv[1]
else:
print >> sys.stderr, usage
exit(1)
if tool == "annotate":
import annotate
success = annotate.main()
elif tool == "extract":
import extract
success = extract.main()
elif tool == "filter":
import filter
success = filter.main()
elif tool == "intersect":
import intersect
success = intersect.main()
elif tool == "indel":
import indel
success = indel.main()
elif tool == "multi":
import multi
success = multi.main()
elif tool == "merge":
import merge
success = merge.main()
elif tool == "sort":
import sort
success = sort.main()
elif tool == "stats":
import stats
success = stats.main()
elif tool == "union":
import union
success = union.main()
elif tool == "unique":
import unique
success = unique.main()
elif tool == "test":
import test
success = test.main()
elif tool == "validate":
import validate
success = validate.main()
elif tool == "--help" or tool == "-h" or tool == "?":
print >> sys.stderr, usage
else:
print >> sys.stderr, "Unknown tool: ",tool
print >> sys.stderr, "\n", usage
exit(1)
# If program completed properly, terminate.
if success == 0: exit(0)
