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Martel based parser to read SAF formatted files. This is a huge regular regular expression for SAF, built using the 'regular expressiona on steroids' capabilities of Martel. http://www.embl-heidelberg.de/predictprotein/Dexa/optin_safDes.html Notes: Just so I remember -- the new end of line syntax is: New regexp syntax - \R \R means " | ?" [\R] means "[ ]" This helps us have endlines be consistent across platforms.
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digits = "0123456789"
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valid_sequence_characters = 'abcdefghijklmnopqrstuvwxyzABCDEFG
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white_space = "\t "
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valid_residue_characters = digits+ white_space+ chr(0x2e)
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residue_number_line = Group("residue_number_line", Rep1(Any(va
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comment_line = Group("comment_line", Str("#")+ ToEol())
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ignored_line = Group("ignored_line", Alt(comment_line, residue
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candidate_line = Group("candidate_line", Assert(Str("#"), 1)+
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saf_record = Group("saf_record", candidate_line+ Rep(Alt(candi
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valid_sequence_characters
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residue_number_line
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ignored_line
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candidate_line
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saf_record
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