Package Bio :: Package NBRF :: Module nbrf_format
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Module nbrf_format

source code

Martel based parser to read NBRF formatted files.

This is a huge regular regular expression for NBRF, built using the 'regular expressiona on steroids' capabilities of Martel.

http://www-nbrf.georgetown.edu/pirwww/pirhome.shtml

Variables [hide private]
  sequence_types = map(Str, valid_sequence_dict.keys())
  sequence_type = Group("sequence_type", Alt(* sequence_types))
  name_line = Martel.Group("name_line", Str(">")+ sequence_type+...
  comment_line = UntilEol("comment")+ AnyEol()
  excluded_chars = '*\n\r'
  sequence_text = Group("sequence_text", Martel.Rep1(AnyBut(excl...
  sequence_line = Group("sequence_line", sequence_text+ AnyEol())
  sequence_final_line = Group("sequence_final_line", UntilSep("s...
  sequence_block = Group("sequence_block", Rep(sequence_line))
  nbrf_record = name_line+ comment_line+ sequence_block+ sequenc...
Variables Details [hide private]

name_line

Value:
Martel.Group("name_line", Str(">")+ sequence_type+ Str(";")+ UntilEol(\
"sequence_name")+ AnyEol())

sequence_text

Value:
Group("sequence_text", Martel.Rep1(AnyBut(excluded_chars)))

sequence_final_line

Value:
Group("sequence_final_line", UntilSep("sequence_final_text", chr(0x2a)\
)+ Str(chr(0x2a))+ Rep1(AnyEol()))

nbrf_record

Value:
name_line+ comment_line+ sequence_block+ sequence_final_line