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import Martel
from Martel import Time
import sprot38
# HAS2_CHICK has a DT line like this
# DT 30-MAY-2000 (REL. 39, Created)
# ^^^ Note the upper-case "REL" instead of "Rel" !
DT_created_exp = (Martel.Str("DT ") +
Time.make_expression("%(DD)-%(Jan)-%(YYYY)") + \
Martel.Re(" \(R[Ee][Ll]. (?P<release>\d\d), Created\)\R"))
OX_start = (Martel.Str("OX NCBI_TaxID=") +
Martel.Rep1(Martel.Digits("ncbi_taxid") +
Martel.Re("[,; ]+")) +
Martel.AnyEol())
OX_cont = (Martel.Str("OX ") +
Martel.Rep1(Martel.Digits("ncbi_taxid") +
Martel.Re("[,; ]+")) +
Martel.AnyEol())
OX_exp = OX_start + Martel.Rep(OX_cont)
# 0 or 1
# in 40 the line changed to look like this
# RX MEDLINE=93305731; PubMed=7916637;
# RX PubMed=11001938;
bib = (Martel.Word("bibliographic_database_name") + Martel.Str("=") +
Martel.ToSep("bibliographic_identifier", ";")
)
RX_exp = (Martel.Str("RX ") + bib +
Martel.Opt(Martel.Str(" ") + bib) +
Martel.AnyEol())
# Here's the neq SQ line format -- uses a CRC64
# SQ SEQUENCE 889 AA; 100368 MW; ABD7E3CD53961B78 CRC64;
SQ_exp = Martel.Re("SQ SEQUENCE +(?P<sequence_length>\d+) AA;" \
" +(?P<molecular_weight>\d+) MW;" \
" +(?P<crc?type=64>\w+) CRC64;\R")
replacements = [
("DT_created", DT_created_exp),
("OX_block", OX_exp),
("RX", RX_exp),
("SQ", SQ_exp),
]
record = Martel.replace_groups(sprot38.record, replacements)
format_expression = Martel.replace_groups(
sprot38.format_expression, replacements)
format = Martel.replace_groups(sprot38.format, replacements)
if __name__ == "__main__":
parser = format.make_parser()
filename = "/home/dalke/ftps/databases/swiss-prot/release_compressed/sprot40.dat"
## import os
## infile = os.popen("zcat " + filename)
infile = open(filename)
infile.seek(107976062)
parser.parseFile(infile)
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