def delimiter(delim):
assert len(delim) == 1, \
"delimiter can only be a single character long, not %s" % repr(delim)
assert delim not in "\n\r", "Cannot use %s as a delimiter" % repr(delim)
field = Martel.Group("field", Martel.Rep(Martel.AnyBut(delim + "\r\n")))
line = field + Martel.Rep(Martel.Str(delim) + field) + Martel.AnyEol()
record = Martel.Group("record", line)
format = Martel.ParseRecords("delimited", {}, record,
RecordReader.CountLines, (1, ))
return format
def test1():
fields = (
["Andrew", "Dalke", "12"],
["Liz", "Nelson", "22"],
["Mandrake", "Moose", "23"],
["Lisa", "Marie", "91"],
)
text = ""
for line in fields:
text = text + string.join(line, " ") + "\n"
format = Martel.Rep1(
Martel.Group("line",
Martel.Word("name", {"type": "first"}) + \
Martel.Spaces() + \
Martel.Word("name", {"type": "last"}) + \
Martel.Spaces() + \
Martel.Integer("age") + \
Martel.AnyEol()
))
iterator = format.make_iterator("line")
i = 0
for record in iterator.iterateString(text, LAX.LAX()):
assert record["name"] == fields[i][:2], (record["name"], fields[i][:2])
assert record["age"] == fields[i][2:3], (record["age"], fields[i][2:3])
i = i + 1
i = 0
for record in iterator.iterateString(text, LAX.LAXAttrs()):
assert [x[0] for x in record["name"]] == fields[i][:2], \
([x[0] for x in record["name"]], fields[i][:2])
assert [x[0] for x in record["age"]] == fields[i][2:3], \
([x[0] for x in record["age"]], fields[i][2:3])
assert record["name"][0][1]["type"] == "first"
assert record["name"][1][1]["type"] == "last"
assert record["age"][0][1].keys() == []
i = i + 1
"""Martel definitions for the output files produced by primer3.
"""
import Martel
any_space = Martel.Re("[ ]+")
blank_line = Martel.AnyEol()
comment_line = Martel.Str("#") + Martel.ToEol()
# comments and blank lines in the file
comments = Martel.Group("comments",
blank_line + comment_line + blank_line + comment_line)
# 1 PRODUCT SIZE: 289
product_size = Martel.Group("product_size", Martel.Re("[\d]+"))
start_primer = Martel.Group(
"start_primer",
any_space + Martel.Re("[\d]+") + Martel.Str(" PRODUCT SIZE: "))
primer_start_line = Martel.Group("primer_start_line",
start_primer + product_size + Martel.AnyEol())
# a blank line that signifies a new primer is coming up
single_primer_line = Martel.Group("single_primer_line", blank_line)
# FORWARD PRIMER 1725 20 59.96 55.00 AGGGAAGGGATGCTAGGTGT
primer_space = Martel.Str(" " * 5)
any_integer = Martel.Re("[\d]+")
any_float = Martel.Re("[\d\.]+")
sequence = Martel.Re("[GATCN]+")
def Simple(tag, tag_data):
return Martel.Group(
tag,
Martel.Str(tag + " ") + Martel.Group(tag_data, Martel.Re("[^\R]*")) +
Martel.AnyEol())
"(?P<secondary_identifier>([^.\R]|(?!.\R)\.)+)")
DR_prosite = Martel.Re("(?P<database_identifier>(PROSITE|PFAM)); " \
"(?P<primary_identifier>[^;]+); " \
"(?P<secondary_identifier>[^;]+); " \
"(?P<status_identifier>[^.]+)")
DR_embl = Martel.Re("(?P<database_identifier>EMBL); " \
"(?P<primary_identifier>[^;]+); " \
"(?P<secondary_identifier>[^;]+); " \
"(?P<status_identifier>[^.]+)")
DR = Martel.Group("DR", Martel.Str("DR ") + \
Martel.Group("database_reference",
Martel.Alt(DR_embl, DR_prosite, DR_general)) + \
Martel.Str(".") + Martel.AnyEol())
DR_block = Martel.Group("DR_block", Martel.Rep1(DR))
#--- KW
KW = Simple("KW", "keyword")
KW_block = Martel.Group("KW_block", Martel.Rep1(KW))
#--- FT
# FT DOMAIN 77 88 ASP/GLU-RICH (ACIDIC).
# 123456789012345678901234567890123456789012345678901234567890123456789012345
# 1 2 3 4 5 6 7
# FT ........ ...... ...... .........................................
# FT 12345678 123456 123456 12345678901234567890123456789012345678901
"""Martel format for primersearch output files,
"""
import Martel
blank_line = Martel.AnyEol()
# Primer name D1S2660
primer_name = Martel.Group("primer_name", Martel.ToEol())
primer_name_line = Martel.Str("Primer name ") + primer_name
# Amplimer 1
amplifier = Martel.Group("amplifier", Martel.Re("[\d]+"))
amplimer_line = Martel.Str("Amplimer ") + amplifier + Martel.AnyEol()
# Sequence: AC074298 AC074298
# Telomere associated sequence for Arabidopsis thaliana TEL1N
# CCGGTTTCTCTGGTTGAAAA hits forward strand at 114 with 0 mismatches
# TCACATTCCCAAATGTAGATCG hits reverse strand at [114] with 0 mismatches
seq_indent = Martel.Str("\t")
sequence_id = Martel.Group("sequence_id", Martel.ToEol())
sequence_descr = Martel.Group("sequence_descr", Martel.ToEol())
sequence_info = sequence_id + sequence_descr
forward_strand_info = Martel.Group("forward_strand_info", Martel.ToEol())
reverse_strand_info = Martel.Group("reverse_strand_info", Martel.ToEol())
amplifier_sequence = Martel.Group(
"amplifier_sequence",
sequence_info + forward_strand_info + reverse_strand_info)
amplifier_sequence_lines = seq_indent + Martel.Str("Sequence: ") + \
amplifier_sequence
