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"""Parser for the SPECLIST.TXT file in SWISS-PROT.
You probably want to use the variables 'record' (for a single record)
and 'format' (for a set of records).
"""
from Martel import *
def SkipLinesToNoEOL(expr):
return Rep(AssertNot(expr) + ToEol()) + expr
DESCRIPTION = Str("Description:") + Spaces() + UntilEol("description") + AnyEol()
NAME = Str("Name:") + Spaces() + UntilEol("name") + AnyEol()
RELEASE = Str("Release:") + Spaces() + UntilEol("release") + AnyEol()
TOTAL_CODES = Str("Total number of organism identification codes currently defined:") + Spaces() + Integer("num_organism_codes") + Str(".") + AnyEol()
TABLE_HEADER = Group("table_header",
Str("Code") + Spaces() + Str("Taxon") + Spaces() +
Str("N=Official name") + ToEol() +
Spaces() + Str("Node") + Spaces() +
Str("C=Common name") + ToEol() +
Spaces() + Str("S=Synonym") + ToEol() +
Rep1(Any(" _")) + AnyEol()
)
_dash_line = Rep1(Str("-")) + AnyEol()
COPYRIGHT = Group("copyright",
_dash_line +
Str("SWISS-PROT is copyright.") + ToEol() +
SkipLinesToNoEOL(_dash_line) +
Rep(AnyEol())
)
_code_line = Group("code", Re(r"[A-Z0-9]{1,5}")) + \
Spaces() + \
Group("kingdom", Any("ABEV")) + \
Spaces() + \
Group("taxon_node", Digits()) + Str(":") + \
Spaces() + \
Str("N=") + Group("official_name", UntilEol()) + \
AnyEol()
_common_line = Spaces() + \
Str("C=") + Group("common_name", UntilEol()) + \
AnyEol()
_synonym_line = Spaces() + \
Str("S=") + Group("synonym", UntilEol()) + \
AnyEol()
record = Group("record",
_code_line + Rep(_common_line) + Rep(_synonym_line)
)
format = Group("format",
SkipLinesToNoEOL(DESCRIPTION) +
NAME +
RELEASE +
SkipLinesToNoEOL(TOTAL_CODES) +
SkipLinesToNoEOL(TABLE_HEADER) +
Rep1(record) +
AnyEol() +
COPYRIGHT
)
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