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

Variable Summary
PrositeAlphabet prosite_alphabet = PrositeAlphabet()
SRE_Pattern prosite_re = ^<?([ABCDEFGHIKLMNPQRSTVWXYZx]|(\[<?[ABCDEF...
SRE_Pattern prosite_term_re = (?:([ABCDEFGHIKLMNPQRSTVWXYZx])|\[(<?)...

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

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]+)\})(?:\((\d+)(,\d+)?\))?$             

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