Package Bio :: Package Prosite :: Module Pattern
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Module Pattern

source code

Classes [hide private]
  PrositeAlphabet
  Prosite
  PrositeTerm
  PrositeMatch
Functions [hide private]
 
prosite_to_re(pattern)
convert a valid Prosite pattern into an re string
source code
 
prosite_to_grouped_re(pattern)
convert a valid Prosite pattern into an re with groups for each term
source code
 
compile(pattern) source code
 
pattern_mapping(prosite, mapping) source code
 
find_terms(pattern) source code
 
verify_pattern(pattern)
returns 1 if the Prosite pattern is syntactically correct, else 0
source code
 
_verify_test(infile)
verify the patterns from a Prosite file handle
source code
Variables [hide private]
  _prosite_trans = '\x00\x01\x02\x03\x04\x05\x06\x07\x08\t\n\x0b...
  prosite_alphabet = PrositeAlphabet()
  prosite_term_re = re.compile(r'(?x)(?:([ABCDEFGHIKLMNPQRSTVWXY...
  prosite_re = re.compile(r'(?x)^<?([ABCDEFGHIKLMNPQRSTVWXYZx]|(...
Variables Details [hide private]

_prosite_trans

Value:
'''\x00\x01\x02\x03\x04\x05\x06\x07\x08\t
\x0b\x0c\r\x0e\x0f\x10\x11\x12\x13\x14\x15\x16\x17\x18\x19\x1a\x1b\x1c\
\x1d\x1e\x1f !"#$%&\'{}*+,-./0123456789:;^=$?@ABCDEFGHIJKLMNOPQRSTUVW.\
YZ[\\]^_`ABCDEFGHIJKLMNOPQRSTUVW.YZ{|]~\x7f\x80\x81\x82\x83\x84\x85\x8\
6\x87\x88\x89\x8a\x8b\x8c\x8d\x8e\x8f\x90\x91\x92\x93\x94\x95\x96\x97\\
x98\x99\x9a\x9b\x9c\x9d\x9e\x9f\xa0\xa1\xa2\xa3\xa4\xa5\xa6\xa7\xa8\xa\
9\xaa\xab\xac\xad\xae\xaf\xb0\xb1\xb2\xb3\xb4\xb5\xb6\xb7\xb8\xb9\xba\\
xbb\xbc\xbd\xbe\xbf\xc0\xc1\xc2\xc3\xc4\xc5\xc6\xc7\xc8\xc9\xca\xcb\xc\
...

prosite_term_re

Value:
re.compile(r'(?x)(?:([ABCDEFGHIKLMNPQRSTVWXYZx])|\[(<?)([ABCDEFGHIKLMN\
PQRSTVWXYZ]+)(>?)\]|\{([ABCDEFGHIKLMNPQRSTVWXYZ]+)\})(?:\((\d+)(,\d+)?\
\))?$')

prosite_re

Value:
re.compile(r'(?x)^<?([ABCDEFGHIKLMNPQRSTVWXYZx]|(\[<?[ABCDEFGHIKLMNPQR\
STVWXYZ]+>?\])|\{[ABCDEFGHIKLMNPQRSTVWXYZ]+\})(\(\d+(,\d+)?\))?(-([ABC\
DEFGHIKLMNPQRSTVWXYZx]|\[[ABCDEFGHIKLMNPQRSTVWXYZ]+>?\]|\{[ABCDEFGHIKL\
MNPQRSTVWXYZ]+\})(\(\d+(,\d+)?\))?)*>?\.$')