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# This was tested against BLOCKS-12.0, June 2000
from Martel import *
from Martel import RecordReader
from Bio import Std
# Header goes up to the line starting with "ID"
header = Rep(AssertNot(Str("ID ")) + \
ToEol())
# ID kringle; BLOCK
# ID 14-3-3; BLOCK
# but not!
# IDSA_METJA|Q58270 ( 46) GGKRIRPYLTV 11
ID = Str("ID ") + Std.dbid(ToSep(sep = ";"), {"type": "primary"}) + \
Str(" BLOCK") + AnyEol()
# AC IPB000001A; distance from previous block=(10,266)
AC = Str("AC ") + Std.dbid(ToSep(sep = ";"), {"type": "accession"}) + \
Str(" distance from previous block=(") + \
Integer("dist1") + Str(",") + Integer("dist2") + \
Str(")") + AnyEol()
# DE Kringle domain
# If the DE line is long, it doen't fold .. it's all on one line
DE = Str("DE ") + ToEol("description")
# BL CCY; width=14; seqs=44; 99.5%=717; strength=1059
BL = Str("BL ") + ToSep("protomat_id", ";") + \
Str(" width=") + Digits("width") + \
Str("; seqs=") + Digits("numseqs") + \
Str("; 99.5%=") + Digits("protomat_count") + \
Str("; strength=") + Digits("strength") + \
AnyEol()
# PLMN_BOVIN|P06868 ( 60) CEEETDFVCRAFQY 26
# ^^^^^^^^^^^^^^^^^
# ^^^^-- number of segments
# ^^^^^^^^^^^^^^-- matching sequence
# ^^-- weight
#
identifier = (Std.dbxref_dbid(UntilSep(sep = "|."),
{"dbname": "swissprot", "type": "primary"}) + \
Str("|") + \
Std.dbxref_dbid(UntilSep(sep = " "),
{"dbname": "swissprot", "type": "accession"})) |\
Std.dbxref_dbid(UntilSep(sep = " "))
segment = AssertNot(Re(r".. ")) + \
identifier + \
Re(r" *\( *") + \
Integer("position") + \
Re(r"\) *") + \
Word("matching_sequence") + Spaces() + \
Digits("weight") + AnyEol()
segment_block = Rep1(segment | AnyEol())
end = Str("//") + AnyEol()
record = Group("record",
ID + AC + DE + BL + segment_block + end)
format_expression = header + Rep1(record)
format = HeaderFooter("dataset", {"format": "blocks/12"},
header, RecordReader.Until, ("ID ",),
record, RecordReader.EndsWith, ("//\n",),
None, None, None)
if __name__ == "__main__":
import os
from xml.sax import saxutils
filename = "/home/dalke/ftps/databases/blocks/unix/blocks-12.0/blocks.dat.Z"
infile = os.popen("zcat " + filename)
parser = format.make_parser(debug_level = 0)
parser.setContentHandler(saxutils.XMLGenerator())
parser.parseFile(infile)
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