base_count_line = Martel.Group("base_count_line",
Martel.Str("BASE COUNT") +
blank_space +
base_count +
Martel.AnyEol())
# ORIGIN
# 1 ggacaaggcc aaggatgctg ctgctgcagc tggagcttcc gcgcaacaag taaacagata
origin_line = Martel.Group("origin_line",
Martel.Str("ORIGIN") +
(Martel.ToEol("origin_name") |
Martel.AnyEol()))
base_number = Martel.Group("base_number",
Martel.Re("[\d]+"))
sequence = Std.sequence(Martel.Group("sequence",
Martel.Re("[\w]+")))
sequence_plus_spaces = Martel.Group("sequence_plus_spaces",
Martel.Rep1(Martel.Str(" ") +
Martel.Opt(sequence)) +
Martel.Opt(Martel.Str(" ")))
sequence_line = Martel.Group("sequence_line",
blank_space +
Martel.Opt(base_number) +
sequence_plus_spaces +
Martel.AnyEol())
sequence_entry = Std.sequence_block(Martel.Group("sequence_entry",
origin_line +
Martel.Rep1(sequence_line)))
# CONTIG
base_count_line = Martel.Group("base_count_line",
Martel.Str("BASE COUNT") +
blank_space +
base_count +
Martel.AnyEol())
# ORIGIN
# 1 ggacaaggcc aaggatgctg ctgctgcagc tggagcttcc gcgcaacaag taaacagata
origin_line = Martel.Group("origin_line",
Martel.Str("ORIGIN") +
(Martel.ToEol("origin_name") |
Martel.AnyEol()))
base_number = Martel.Group("base_number",
Martel.Re("[\d]+"))
sequence = Std.sequence(Martel.Re(r"[\w ]+"))
sequence_line = Martel.Group("sequence_line",
blank_space +
Martel.Opt(base_number) +
sequence +
Martel.AnyEol())
sequence_entry = Std.sequence_block(origin_line +
Martel.Rep1(sequence_line))
# CONTIG
# this is the contig information for RefSeq records
contig_location = Martel.Group("contig_location",
Martel.ToEol("feature_location") + \
#--- SQ
# SQ SEQUENCE XXXX AA; XXXXX MW; XXXXX CRC32;
# (Those X's don't really indicate the size)
SQ = Martel.Group("SQ",
Martel.Re("SQ SEQUENCE +(?P<sequence_length>\d+) AA;" \
" +(?P<molecular_weight>\d+) MW;" \
" +(?P<crc?type=32>\w+) CRC32;\R")
)
##SQ_data = Martel.Group("SQ_data",
## Martel.Re(" (?P<sequence>[^\R]*)\R"))
SQ_data = Martel.Str(" ") + \
Std.sequence(Martel.UntilEol()) + \
Martel.AnyEol()
##sequence = Martel.Group("sequence_block", Martel.Group("SQ_data_block",
## SQ + Martel.Rep(SQ_data)))
sequence = Std.sequence_block(SQ + Martel.Rep(SQ_data),
{"alphabet": "iupac-ambiguous-protein"})
#--- //
end = Martel.Group("END", Martel.Str("//") + Martel.AnyEol())
####################### put it all together
record = Std.record(
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 + \
# "|" them all together
ncbi_word = Std.dbxref(reduce(operator.or_, ids))
#ncbi_term = Assert(Re("[^ \R]+\|")) + \
ncbi_term = ncbi_word + Rep(Str("|") + ncbi_word)
# Anything else
generic_term = Std.dbxref(
Std.dbxref_dbid(UntilSep(sep = " "), {"dbname": "local"})
)
id_term = ncbi_term | generic_term
###########################################################
comment_lines = Rep(Str("#") + ToEol())
title = Str(">") + Std.description_line(id_term + UntilEol()) + AnyEol()
seqline = AssertNot(Str(">")) + Std.sequence(UntilEol()) + AnyEol()
# can get a sequence line without an Eol at the end of a file
seqline_nonewline = AssertNot(Str(">")) + Std.sequence(Word())
sequence = Std.sequence_block(Rep(seqline | seqline_nonewline))
record = Std.record(comment_lines + title + sequence + Rep(AnyEol()))
# define a format which reads records, but allows #-style comments in
# the FASTA file
format = HeaderFooter("dataset", {"format": "fasta"},
comment_lines, RecordReader.Until, (">",),
record, RecordReader.StartsWith, (">",),
comment_lines, RecordReader.Everything, ()
)
