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

Classes
Prosite  
PrositeAlphabet  
PrositeMatch  
PrositeTerm  

Function Summary
  compile(pattern)
  find_terms(pattern)
  pattern_mapping(prosite, mapping)
  prosite_to_grouped_re(pattern)
convert a valid Prosite pattern into an re with groups for each term
  prosite_to_re(pattern)
convert a valid Prosite pattern into an re string
  verify_pattern(pattern)
returns 1 if the Prosite pattern is syntactically correct, else 0
  _verify_test(infile)
verify the patterns from a Prosite file handle

Variable Summary
PrositeAlphabet prosite_alphabet = PrositeAlphabet()
SRE_Pattern prosite_re = ^<?([ABCDEFGHIKLMNPQRSTVWXYZx]|(\[<?[ABCDEF...
SRE_Pattern prosite_term_re = (?:([ABCDEFGHIKLMNPQRSTVWXYZx])|\[(<?)...
str _prosite_trans = '\x00\x01\x02\x03\x04\x05\x06\x07\x08\t...

Function Details

prosite_to_grouped_re(pattern)

convert a valid Prosite pattern into an re with groups for each term

prosite_to_re(pattern)

convert a valid Prosite pattern into an re string

verify_pattern(pattern)

returns 1 if the Prosite pattern is syntactically correct, else 0

_verify_test(infile)

verify the patterns from a Prosite file handle

Variable Details

prosite_alphabet

Type:
PrositeAlphabet
Value:
PrositeAlphabet()                                                      

prosite_re

Type:
SRE_Pattern
Value:
^<?([ABCDEFGHIKLMNPQRSTVWXYZx]|(\[<?[ABCDEFGHIKLMNPQRSTVWXYZ]+>?\])|\{\
[ABCDEFGHIKLMNPQRSTVWXYZ]+\})(\(\d+(,\d+)?\))?(-([ABCDEFGHIKLMNPQRSTVW\
XYZx]|\[[ABCDEFGHIKLMNPQRSTVWXYZ]+>?\]|\{[ABCDEFGHIKLMNPQRSTVWXYZ]+\})\
(\(\d+(,\d+)?\))?)*>?\.$                                               

prosite_term_re

Type:
SRE_Pattern
Value:
(?:([ABCDEFGHIKLMNPQRSTVWXYZx])|\[(<?)([ABCDEFGHIKLMNPQRSTVWXYZ]+)(>?)\
\]|\{([ABCDEFGHIKLMNPQRSTVWXYZ]+)\})(?:\((\d+)(,\d+)?\))?$             

_prosite_trans

Type:
str
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\
...                                                                    

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