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 test_reader_parser():
record = Martel.Group("start", Martel.Rep(Martel.Str("abc"))) + \
Martel.Group("end", Martel.Rep(Martel.Str("xyz")))
parser = record.make_parser()
parser = Parser.Parser(parser.tagtable)
parser.setErrorHandler(handler.ErrorHandler())
parser.parseString("abc" * 10 + "xyz")
try:
parser.parseString("abc" * 10 + "xyzQ")
except Parser.ParserPositionException:
pass
else:
raise AssertionError, "didn't get a position exception"
try:
parser.parseString("abc" * 10 + "x")
except Parser.ParserPositionException:
pass
else:
raise AssertionError, "didn't get a position exception"
def test_record_parser():
record = Martel.Group("A", Martel.Str("X\n") + Martel.Re("a*\n"))
p = record.make_parser()
parser = Parser.RecordParser("blah", {}, p.tagtable, (0, 1, {}),
RecordReader.StartsWith, ("X", ))
err = CountErrors()
parser.setErrorHandler(err)
count = CountRecords("A")
parser.setContentHandler(count)
parser.parseString("X\na\nX\nb\nX\naaa\nX\naaaa\nX\nq\nX\na\n")
assert err.fatal_error_count == 0, err.fatal_error_count
assert err.error_count == 2, err.error_count
assert count.count == 4, count.count
"""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())
DR_general = Martel.Re("(?P<database_identifier>[^;]+);" \
"(?P<primary_identifier>[^;]+); " \
"(?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
# Copyright 2001 by Katharine Lindner. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Martel regular expression for Intelligenetic format (DEPRECATED).
This is a huge regular regular expression for the IntelliGenetics/MASE format,
built using the 'regular expressions on steroids' capabilities of Martel.
"""
#http://immuno.bme.nwu.edu/seqhunt.html
# Martel
import Martel
# --- first set up some helper constants and functions
comment_line = Martel.Group( "comment_line", \
Martel.Str( ';' ) +
Martel.ToEol( "comment" ) )
comment_lines = Martel.Group("comment_lines", Martel.Rep(comment_line))
title_line = Martel.Group( "title_line", \
Martel.Expression.Assert( Martel.Str( ';' ), 1 ) +
Martel.ToEol() )
residue_line = Martel.Group( "residue_line", \
Martel.Expression.Assert( Martel.Str( ';' ), 1 ) +
Martel.ToEol( "sequence" ) )
residue_lines = Martel.Group("residue_lines", Martel.Rep1(residue_line))
intelligenetics_record = comment_lines + title_line + residue_lines
def test_single():
ele = get_element(
Martel.Group("spam", Martel.Str("X"), {"format": "swissprot"}))
check_element(ele, ("spam", {"format": "swissprot"}))
def test_none():
ele = get_element(Martel.Group("spam", Martel.Str("X")))
check_element(ele, ("spam", {}))
ele = get_element(Martel.Group("spam", Martel.Str("X"), {}))
check_element(ele, ("spam", {}))
"""Example of registering a database with the Biopython-specific system.
"""
from Bio.sources import CGI
local_cgi = CGI(name = "local_cgi",
delay = 0.0,
cgi = "http://www.myserver.org/cgi-bin/my_local.cgi",
url = "http://www.myserver.org/cgi_documentation.html",
doc = "Query a local databases",
failure_cases = [])
import Martel
my_failures = [
(Martel.Str("Sequence not available"), "No sequence found")]
from Bio import register_db
register_db(name = "nucleotide-genbank-local",
key = "uid",
source = local_cgi,
failure = my_failures)
register_db(name = "genbank", behavior = "concurrent")
from Bio import group_db
group_db("genbank", "nucleotide-genbank-local")
group_db("genbank", "nucleotide-genbank-cgi")
from Bio import db
print db.keys()
"""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