def test_write(self) : f = StringIO(plain_io.example) seqs = plain_io.read(f) fout = StringIO() null_io.write(fout,seqs) fout.seek(0) self.assertEqual(fout.read(), '')
def test_write(self): f = StringIO(plain_io.example) seqs = plain_io.read(f) fout = StringIO() null_io.write(fout, seqs) fout.seek(0) self.assertEqual(fout.read(), '')
def test_write_seq(self): f = StringIO(array_io.example) seqs = array_io.read(f) fout = StringIO() array_io.write(fout, seqs) fout.seek(0) seqs2 = array_io.read(fout) self.assertEqual(seqs, seqs2)
def test_write_comments(self): f = StringIO(example_with_optional_comments) seqs = fasta_io.read(f) fout = StringIO() fasta_io.write(fout, seqs) fout.seek(0) seqs2 = fasta_io.read(fout) self.assertEqual(seqs, seqs2) self.assertEqual(seqs[1].description, seqs2[1].description)
def test_write_comments(self) : f = StringIO(example_with_optional_comments) seqs = fasta_io.read(f) fout = StringIO() fasta_io.write(fout, seqs) fout.seek(0) seqs2 = fasta_io.read(fout) self.assertEqual(seqs, seqs2) self.assertEqual(seqs[1].description, seqs2[1].description)
def test_write(self): f = StringIO(clustal_io.example) seqs = clustal_io.read(f) fout = StringIO() clustal_io.write(fout, seqs) fout.seek(0) seqs2 = clustal_io.read(fout) self.assertEqual(seqs, seqs2) f.close()
def test_write_seq(self) : f = StringIO(plain_io.example) seqs = plain_io.read(f) fout = StringIO() plain_io.write(fout,seqs) fout.seek(0) seqs2 = plain_io.read(fout) #print seqs[0].alphabet !=seqs2[0].alphabet self.assertEqual(seqs[0].alphabet, seqs2[0].alphabet) self.assertEqual(seqs[0], seqs2[0]) self.assertEqual(seqs, seqs2)
def test_write_seq(self): f = StringIO(plain_io.example) seqs = plain_io.read(f) fout = StringIO() plain_io.write(fout, seqs) fout.seek(0) seqs2 = plain_io.read(fout) #print seqs[0].alphabet !=seqs2[0].alphabet self.assertEqual(seqs[0].alphabet, seqs2[0].alphabet) self.assertEqual(seqs[0], seqs2[0]) self.assertEqual(seqs, seqs2)
def read_seq_data(fin, input_parser=seq_io.read, alphabet=None, ignore_lower_case=False, max_file_size=0): """ Read sequence data from the input stream and return a seqs object. The environment variable WEBLOGO_MAX_FILE_SIZE overides the max_file_size argument. Used to limit the load on the WebLogo webserver. """ max_file_size = int(os.environ.get("WEBLOGO_MAX_FILE_SIZE", max_file_size)) # If max_file_size is set, or if fin==stdin (which is non-seekable), we # read the data and replace fin with a StringIO object. if (max_file_size > 0): data = fin.read(max_file_size) more_data = fin.read(2) if more_data != "": raise IOError("File exceeds maximum allowed size: %d bytes" % max_file_size) fin = StringIO(data) elif fin == sys.stdin: fin = StringIO(fin.read()) fin.seek(0) seqs = input_parser(fin) if seqs is None or len(seqs) == 0: raise ValueError("Please provide a multiple sequence alignment") if ignore_lower_case: # Case is significant. Do not count lower case letters. for i, s in enumerate(seqs): seqs[i] = s.mask() # Add alphabet to seqs. if alphabet: seqs.alphabet = Alphabet(alphabet) else: seqs.alphabet = Alphabet.which(seqs) return seqs
def read_seq_data(fin, input_parser=seq_io.read, alphabet=None, ignore_lower_case=False, max_file_size=0): """ Read sequence data from the input stream and return a seqs object. The environment variable WEBLOGO_MAX_FILE_SIZE overides the max_file_size argument. Used to limit the load on the WebLogo webserver. """ max_file_size =int(os.environ.get("WEBLOGO_MAX_FILE_SIZE", max_file_size)) # If max_file_size is set, or if fin==stdin (which is non-seekable), we # read the data and replace fin with a StringIO object. if(max_file_size>0) : data = fin.read(max_file_size) more_data = fin.read(2) if more_data != "" : raise IOError("File exceeds maximum allowed size: %d bytes" % max_file_size) fin = StringIO(data) elif fin == sys.stdin: fin = StringIO(fin.read()) fin.seek(0) seqs = input_parser(fin) if seqs is None or len(seqs) ==0 : raise ValueError("Please provide a multiple sequence alignment") if ignore_lower_case : # Case is significant. Do not count lower case letters. for i,s in enumerate(seqs) : seqs[i] = s.mask() # Add alphabet to seqs. if alphabet : seqs.alphabet = Alphabet(alphabet) else : seqs.alphabet = Alphabet.which(seqs) return seqs