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How to use test_readfile method in avocado

Best Python code snippet using avocado_python

test_FileIO.py

Source:test_FileIO.py

...4class TestPepXML(unittest.TestCase):5    def setUp(self):6        dirname = os.path.dirname(os.path.abspath(__file__))7        self.filename = os.path.join(dirname, "test.pep.xml").encode()8    def test_readfile(self):9        pepxml_file = pyopenms.PepXMLFile()10        peps = []11        prots = []12        pepxml_file.load(self.filename, prots, peps)13    def test_readfile_content(self):14        pepxml_file = pyopenms.PepXMLFile()15        peps = []16        prots = []17        pepxml_file.load(self.filename, prots, peps)18        self.assertEqual( len(prots),  1)19        self.assertEqual( len(peps),  3)20        self.assertEqual( peps[0].getHits()[0].getSequence().toString(), b"LAPSAAEDGAFR")21class TestIdXML(unittest.TestCase):22    def setUp(self):23        dirname = os.path.dirname(os.path.abspath(__file__))24        self.filename = os.path.join(dirname, "test.idXML").encode()25    def test_readfile(self):26        idxml_file = pyopenms.IdXMLFile()27        peps = []28        prots = []29        idxml_file.load(self.filename, prots, peps)30    def test_readfile_content(self):31        idxml_file = pyopenms.IdXMLFile()32        peps = []33        prots = []34        idxml_file.load(self.filename, prots, peps)35        self.assertEqual( len(prots),  1)36        self.assertEqual( len(peps),  3)37class TestIndexedMzMLFileLoader(unittest.TestCase):38    def setUp(self):39        dirname = os.path.dirname(os.path.abspath(__file__))40        self.filename = os.path.join(dirname, "test.indexed.mzML").encode()41    def test_readfile(self):42        e = pyopenms.OnDiscMSExperiment();43        success = pyopenms.IndexedMzMLFileLoader().load(self.filename, e)44        self.assertTrue(success)45    def test_readfile_content(self):46        e = pyopenms.OnDiscMSExperiment();47        pyopenms.IndexedMzMLFileLoader().load(self.filename, e)48        self.assertEqual( e.getNrSpectra() ,  2)49        self.assertEqual( e.getNrChromatograms() ,  1)50        s = e.getSpectrum(0)51        data_mz, data_int = s.get_peaks()52        self.assertEqual( len(data_mz), 19914)53        self.assertEqual( len(data_int), 19914)54        self.assertEqual( len(e.getSpectrum(1).get_peaks()[0]), 19800)55        self.assertEqual( len(e.getSpectrum(1).get_peaks()[1]), 19800)56        self.assertEqual( len(e.getChromatogram(0).get_peaks()[0]), 48)57        self.assertEqual( len(e.getChromatogram(0).get_peaks()[1]), 48)58        raised = False59        try:60            e.getChromatogram(2).get_peaks()61        except Exception as e:62            raised = True63        self.assertTrue(raised)64class TestIndexedMzMLFile(unittest.TestCase):65    def setUp(self):66        dirname = os.path.dirname(os.path.abspath(__file__))67        self.filename = os.path.join(dirname, "test.indexed.mzML").encode()68    def test_readfile(self):69        f = pyopenms.IndexedMzMLFile()70        f.openFile(self.filename)71        self.assertTrue(f.getParsingSuccess())72    def test_readfile_content(self):73        f = pyopenms.IndexedMzMLFile()74        f.openFile(self.filename)75        self.assertEqual( f.getNrSpectra() ,  2)76        self.assertEqual( f.getNrChromatograms() ,  1)77        s = f.getSpectrumById(0)78        mzdata = s.getMZArray()79        intdata = s.getIntensityArray()80        self.assertEqual( len(mzdata), 19914)81        self.assertEqual( len(intdata), 19914)82if __name__ == '__main__':...

class04_files.py

Source:class04_files.py

1#### Class 032#### Reading and writing files3## Reading text files ------------------------------------------------4import sys5## Read all lines as one string6with open('test_readfile.txt') as f:7  the_whole_thing = f.read()8  print the_whole_thing9## Read line by line10with open('test_readfile.txt') as f:11  lines_list = f.readlines()12  for l in lines_list:13    print l14## More efficiently we can loop over the file object15## (i.e. we don't need the variable lines)16with open('test_readfile.txt') as f:   17  for l in f:18    print l19    20    21## We can also manually open and close files,22## now we need to handle exceptions and close23## I never do this24f =  open('test_readfile.txt')25print f.read()26f.close()27## Writing text files ------------------------------------------------28## Writing files is easy,29## open command takes r, w, a, plus some others30with open('test_writefile.txt', 'w') as f:31  ## wipes the file clean and opens it32  f.write("Hi guys.")33  f.write("Does this go on the second line?")34  f.writelines(['a\n', 'b\n', 'c\n'])35with open('test_writefile.txt', 'a') as f:36  ## appends37  f.write("I got appended!")38## Writing csv files ------------------------------------------------39import csv40## Open a file stream and create a CSV writer object41with open('test_writecsv.txt', 'wb') as f:42  my_writer = csv.writer(f)43  for i in range(1, 100):44    my_writer.writerow([i, i-1])45## Now read in the csv46with open('test_writecsv.txt', 'rb') as f:47  my_reader = csv.reader(f)48  mydat = []49  for row in my_reader:50    mydat.append(row)51print mydat52    53## Adding column names54with open('test_csvfields.txt', 'wb') as f:55  my_writer = csv.DictWriter(f, fieldnames = ("A", "B"))56  my_writer.writeheader()57  for i in range(1, 100):58    my_writer.writerow({"B":i, "A":i-1})59    60    61with open('test_csvfields.csv', 'rb') as f:62  my_reader = csv.DictReader(f)63  for row in my_reader:64    print row65# Copyright (c) 2014 Matt Dickenson66# 67# Permission is hereby granted, free of charge, to any person obtaining a copy68# of this software and associated documentation files (the "Software"), to deal69# in the Software without restriction, including without limitation the rights70# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell71# copies of the Software, and to permit persons to whom the Software is72# furnished to do so, subject to the following conditions:73# 74# The above copyright notice and this permission notice shall be included in all75# copies or substantial portions of the Software.76# 77# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR78# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,79# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE80# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER81# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,82# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE...

tt.py

Source:tt.py

1import os2def test_readfile(filepath):3    """4    :param filepath:5    :return:6    """7    with open(filepath, "r") as r:8        return r.readlines()9# def getallfiles(path):10#     allfile=[]11#     for dirpath, dirnames, filenames in os.walk(path):12#         for dir in dirnames:13#             allfile.append(os.path.join(dirpath,dir))14#         for name in filenames:15#             allfile.append(os.path.join(dirpath, name))16#     return allfile17#18#19# if __name__ == '__main__':20#     path = "D:\qycache"21#     allfile = getallfiles(path)22#     for file in allfile:23#         print(file)24if __name__ == '__main__':25    path = "2020_09_28 æ¡è±ææ æ¯å®£è¨177GBåé2020_09_28 æ¡è±ææ æ¯å®£è¨177GBåé_2.jpg"26    print(test_readfile(path))27    if len(test_readfile(path)) == 0:  # ç©ºæä»¶ï¼å é¤...

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