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"""Format from EMBL Nucleotide Sequence Database Release 65, December 2000
"""
import Martel
from Martel import RecordReader, Time
from Bio import Std
from Bio.expressions.swissprot import sprot38
whitespace = Martel.Spaces()
## ID - identification (begins each entry; 1 per entry)
# ID entryname dataclass; molecule; division; sequencelength BP.
divisions = Martel.Re("EST|PHG|FUN|GSS|HTC|HTG|HUM|INV|ORG|MAM|VRT|PLN|" + \
"PRO|ROD|SYN|STS|UNC|VRL|[A-Z]{3}")
# XXX is found in S40706
ID_line = Martel.Str("ID ") + \
Std.dbid(Martel.UntilSep("entry_name", " "), {"type": "primary",
"dbname": "embl"}) + \
whitespace + \
Martel.ToSep("dataclass", ";") + \
whitespace + \
Martel.Group("molecule",
Std.alphabet(Martel.Str("DNA", "circular DNA"),
{"alphabet": "iupac-ambiguous-dna"}) |
Std.alphabet(Martel.Str("RNA", "circular RNA"),
{"alphabet": "iupac-ambiguous-rna"}) |
Std.alphabet(Martel.Str("XXX"),
{"alphabet": "nucleotide"})) + \
Martel.Str("; ") + \
Martel.Group("division", divisions) + \
Martel.Str("; ") + \
Martel.Digits("length") + \
Martel.Str(" BP.") + \
Martel.AnyEol()
## AC - accession number (>=1 per entry)
accession = Std.dbid(Martel.UntilSep("accession", ";"),
{"type": "accession",
"dbname": "embl"}) + Martel.Str(";")
AC_line = Martel.Str("AC ") + \
accession + Martel.Rep(Martel.Str(" ") + accession) + \
Martel.AnyEol()
AC_block = Martel.Rep1(AC_line)
## SV - sequence version (1 per entry)
SV_line = Martel.Str("SV ") + \
Martel.Group("sequence_version",
Martel.ToSep("accession", ".") + \
Martel.Digits("version")) + \
Martel.AnyEol()
## DT - date (2 per entry)
date = Time.make_expression("%(day)-%(Jan)-%(year)")
DT_created_line = Martel.Str("DT ") + \
Martel.Group("date_created", date) + \
Martel.Str(" (Rel. ") + \
Martel.Digits("release_created") + \
Martel.Str(", Created)") + \
Martel.AnyEol()
DT_updated_line = Martel.Str("DT ") + \
Martel.Group("date_updated", date) + \
Martel.Str(" (Rel. ") + \
Martel.Digits("release_updated") + \
Martel.Str(", Last updated, Version ") + \
Martel.Digits("version_number") + \
Martel.Str(")") + \
Martel.AnyEol()
DT_block = DT_created_line + DT_updated_line
## DE - description (>=1 per entry)
DE_line = Martel.Str("DE ") + \
Std.description(Martel.UntilEol("description")) + \
Martel.AnyEol()
DE_block = Std.description_block(Martel.Group("description_block",
Martel.Rep1(DE_line)))
## KW - keyword (>=1 per entry)
KW_line = Martel.Str("KW ") + \
Martel.ToEol("keyword_data")
KW_block = Martel.Rep1(KW_line)
## OS - organism species (>=1 per entry)
OS_block = sprot38.OS_block
## OC - organism classification (>=1 per entry)
OC_block = sprot38.OC_block
## OG - organelle (0 or 1 per entry)
OG_block = sprot38.OG_block
organism = Martel.Group("organism",
OS_block + \
OC_block + \
Martel.Opt(OG_block))
## RN - reference number (>=1 per entry)
## RC - reference comment (>=0 per entry)
## RP - reference positions (>=1 per entry)
## RX - reference cross-reference (>=0 per entry)
## RA - reference author(s) (>=1 per entry)
## RT - reference title (>=1 per entry)
## RL - reference location (>=1 per entry)
RN_line = sprot38.RN
RC_block = sprot38.RC_block
RP_line = sprot38.RP
RX_line = sprot38.RX
RX_block = Martel.Group("RX_block", Martel.Rep1(RX_line))
RA_block = sprot38.RA_block
RT_block = sprot38.RT_block
RL_block = sprot38.RL_block
reference = Martel.Group("reference",
RN_line + \
Martel.Opt(RC_block) + \
Martel.Opt(RP_line) + \
Martel.Opt(RX_block) + \
RA_block + \
RT_block + \
RL_block)
## DR - database cross-reference (>=0 per entry)
DR_block = sprot38.DR_block
## FH - feature table header (0 or 2 per entry)
FH_block = Martel.Str("FH Key Location/Qualifiers") + \
Martel.AnyEol() + \
Martel.Str("FH") + \
Martel.AnyEol()
## FT - feature table data (>=0 per entry)
##FT_line = Martel.Str("FT ") + \
## Martel.ToEol("ft_data")
##FT_block = Martel.Rep1(FT_line)
fq_dbxref = Std.feature_qualifier_name(Martel.Str("db_xref")) + \
Martel.Str('=') + \
Std.feature_qualifier_description(
Martel.Str('"') + \
Std.dbxref(Std.dbxref_dbname(Martel.UntilSep(None, ":")) + \
Martel.Str(":") + \
Std.dbxref_dbid(Martel.UntilSep(None, '"'))) + \
Martel.Str('"')) + \
Martel.AnyEol()
fq_generic = \
Martel.Assert(Martel.Word() + Martel.Str("=")) + \
Std.feature_qualifier_name(Martel.Word()) + \
Martel.Str("=") + \
Std.feature_qualifier_description(Martel.UntilEol()) + \
Martel.AnyEol() + \
Martel.Rep(
Martel.Str("FT ") + \
(Martel.AssertNot(Martel.Str("/")) |
Martel.AssertNot(Martel.Re(r"/\w+="))) + \
Std.feature_qualifier_description(Martel.UntilEol()) + \
Martel.AnyEol())
feature_qualifier = Std.feature_qualifier(
Martel.Str("FT /") + \
(fq_dbxref | fq_generic))
feature = Std.feature(
Martel.Str("FT ") + \
Std.feature_name(Martel.UntilSep(sep = " ")) + \
whitespace + \
Std.feature_location(Martel.UntilEol()) + \
Martel.AnyEol() + \
Martel.Rep(Martel.Str("FT ") + \
Martel.AssertNot(Martel.Str("/")) + \
Std.feature_location(Martel.UntilEol()) + \
Martel.AnyEol()
) + \
Martel.Rep(feature_qualifier)
)
FT_block = Std.feature_block(Martel.Rep(feature),
{"location-style": "genbank"})
## CC - comments or notes (>=0 per entry)
CC_line = Martel.Str("CC ") + \
Martel.ToEol("comment")
CC_block = Martel.Rep1(CC_line)
## XX - spacer line (many per entry)
XX = Martel.Str("XX") + Martel.AnyEol()
## SQ - sequence header (1 per entry)
SQ_line = Martel.Str("SQ Sequence ") + \
Martel.Digits("num_BP") + \
Martel.Str(" BP; ") + \
Martel.Digits("num_A") + \
Martel.Str(" A; ") + \
Martel.Digits("num_C") + \
Martel.Str(" C; ") + \
Martel.Digits("num_G") + \
Martel.Str(" G; ") + \
Martel.Digits("num_T") + \
Martel.Str(" T; ") + \
Martel.Digits("num_other") + \
Martel.Str(" other;") + \
Martel.AnyEol()
## bb - (blanks) sequence data (>=1 per entry)
SQ_data = Martel.Str(" ") + \
Std.sequence(Martel.Re(".{65}")) + \
whitespace + \
Martel.Digits("end_position") + \
Martel.AnyEol()
SQ_block = Std.sequence_block(SQ_line + Martel.Rep1(SQ_data))
## // - termination line (ends each entry; 1 per entry)
end = Martel.Str("//") + Martel.AnyEol()
record = Martel.Group("record", \
ID_line + \
Martel.Opt(XX) + \
AC_block + \
Martel.Opt(XX) + \
SV_line + \
Martel.Opt(XX) + \
DT_block + \
Martel.Opt(XX) + \
DE_block + \
Martel.Opt(XX) + \
KW_block + \
Martel.Opt(XX) + \
Martel.Rep1(organism + Martel.Opt(XX)) + \
Martel.Rep(reference + Martel.Opt(XX)) + \
Martel.Opt(DR_block + \
Martel.Opt(XX)) + \
Martel.Rep(CC_block + \
Martel.Opt(XX)) + \
FH_block + \
FT_block + \
Martel.Opt(XX) + \
SQ_block + \
end,
{"format": "embl/65"})
format_expression = Martel.Group("dataset", Martel.Rep1(record),
{"format": "embl/65"})
format = Martel.ParseRecords("dataset", {"format": "embl/65"},
record, RecordReader.EndsWith, ("//\n",) )
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