nid +
Martel.AnyEol())
# PID g6754304
pid = Martel.Group("pid",
Martel.Re("[\w\d]+"))
pid_line = Martel.Group("pid_line",
Martel.Str("PID") +
blank_space +
pid +
Martel.AnyEol())
# version and GI line
# VERSION AC007323.5 GI:6587720
version = Martel.Group("version",
Std.dbid(Martel.Re("[\w\d\.]+"),
{"type" : "primary", "dbname" : "genbank"}))
gi = Martel.Group("gi",
Std.dbid(Martel.Re("[\d]+"),
{"type" : "secondary", "dbname" : "genbank"}))
version_line = Martel.Group("version_line",
Martel.Str("VERSION") +
blank_space +
version +
Martel.Opt(blank_space +
Martel.Str("GI:") +
gi) +
Martel.AnyEol())
# DBSOURCE REFSEQ: accession NM_010510.1
"""
import warnings
warnings.warn("Bio.expressions was deprecated, as it does not work with recent versions of mxTextTools. If you want to continue to use this module, please get in contact with the Biopython developers at [email protected] to avoid permanent removal of this module from Biopython", DeprecationWarning)
from Bio import Std
import Martel
from Martel import Time
import sprot40
# The ID line contains a versioned period number
ID_exp = Martel.Group("ID",
Martel.Str("ID ") + \
Std.dbid(Martel.Group("entry_name", Martel.Re("[\w.]+")),
{"type": "primary", "dbname": "sp"}) + \
Martel.Spaces() + \
Martel.Word("data_class_table") + \
Martel.Str(";") + Martel.Spaces() + \
Martel.Word("molecule_type") + \
Martel.Str(";") + Martel.Spaces() + \
Martel.Digits("sequence_length") + \
Martel.Str(" AA.") + \
Martel.AnyEol()
)
# The DT formatted lines look different, and there is not
# a third DT line for annotations
# DT 04-MAR-2003 (IPI Human rel. 2.17, Created)
# DT 04-MAR-2003 (IPI Human rel. 2.17, Last sequence update)
o block_data - A callback tag for the data in the block (ie. the
stuff you are interested in).
"""
diff = INDENT - len(identifier)
assert diff > 0, diff
return Martel.Group(block_tag,
Martel.Str(identifier + " " * diff) +
Martel.ToEol(block_data) +
Martel.Rep(Martel.AnyEol() |
(Martel.Str(" " * INDENT) + Martel.ToEol(block_data))))
# The first line
# LOCUS AC007323 86436 bp DNA PLN 19-JAN-2000
locus = Std.dbid(Martel.Word(), {"dbname": "gb", "type": "primary"})
size = Martel.Group("size",
Martel.Rep1(Martel.Integer()))
# deal with the different kinds of residues we can have
residue_prefixes = Martel.Str("ss-", "ds-", "ms-")
residue_types = [
Std.alphabet(Martel.Str("DNA"), {"alphabet": "iupac-ambiguous-dna"}),
Std.alphabet(Martel.Str("RNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("mRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("tRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("rRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("uRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("snRNA"), {"alphabet": "iupac-ambiguous-rna"}),
Std.alphabet(Martel.Str("PROTEIN"), {"alphabet": "iupac-protein"}),
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.") + \
import Martel
from Martel import RecordReader, Time
from Bio import Std
def Simple(tag, tag_data):
return Martel.Group(tag,
Martel.Str(tag + " ") + \
Martel.ToEol(tag_data)
)
#--- ID
ID = Martel.Group("ID",
Martel.Str("ID ") + \
Std.dbid(Martel.Word("entry_name"), {"type": "primary",
"dbname": "sp"}) + \
Martel.Spaces() + \
Martel.Word("data_class_table") + \
Martel.Str(";") + Martel.Spaces() + \
Martel.Word("molecule_type") + \
Martel.Str(";") + Martel.Spaces() + \
Martel.Digits("sequence_length") + \
Martel.Str(" AA.") + \
Martel.AnyEol()
)
#--- AC
AC = Martel.Group("AC",
Martel.Str("AC ") + \
Std.dbid(Martel.Word("ac_number"),
{"type": "accession",
warnings.warn("Bio.expressions was deprecated, as it does not work with recent versions of mxTextTools. If you want to continue to use this module, please get in contact with the Biopython developers at [email protected] to avoid permanent removal of this module from Biopython", DeprecationWarning)
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
