Bio.Prosite.Pattern

Package Bio :: Package Prosite :: Module Pattern

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Module Bio.Prosite.Pattern

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

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

convert a valid Prosite pattern into an re string

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

verify the patterns from a Prosite file handle

Variable Details

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

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

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\ ...

Generated by Epydoc 2.1 on Mon Aug 14 08:26:41 2006