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Imported modules
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from Bio import Seq, Alphabet
import re
import string
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Functions
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_verify_test
compile
find_terms
pattern_mapping
prosite_to_grouped_re
prosite_to_re
verify_pattern
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_verify_test
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_verify_test ( infile )
verify the patterns from a Prosite file handle
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compile
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compile ( pattern )
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Exceptions
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TypeError, "not a legal prosite pattern"
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find_terms
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find_terms ( pattern )
This does not verify the pattern is correct - invalid patterns can
be converted!
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Exceptions
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TypeError, "[<] only allowed for first term (%s)" % repr( term )
TypeError, "[>] only allowed for last term (%s)" % repr( term )
TypeError, "not a Prosite term (%s)" % repr( term )
TypeError, "not a prosite pattern - needs a final '.'"
TypeError, "not a prosite term (%s)" % repr( term )
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pattern_mapping
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pattern_mapping ( prosite, mapping )
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prosite_to_grouped_re
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prosite_to_grouped_re ( pattern )
convert a valid Prosite pattern into an re with groups for each term
This does not verify the pattern is correct - invalid patterns can
be converted!
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prosite_to_re
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prosite_to_re ( pattern )
convert a valid Prosite pattern into an re string
This does not verify that the pattern is correct - invalid patterns
can be converted!
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verify_pattern
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verify_pattern ( pattern )
returns 1 if the Prosite pattern is syntactically correct, else 0
This verifies the pattern is correct.
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Classes
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