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"""Code to interact with various Primer-related programs from EMBOSS.
"""
# standard library
import string
from xml.sax import handler
# Martel
import Martel
from Martel import RecordReader
# biopython stuff
from Bio.ParserSupport import AbstractConsumer
from Bio.ParserSupport import EventGenerator
import primersearch_format
import primer3_format
# --- primersearch
class PrimerSearchInputRecord:
"""Represent the input file into the primersearch program.
This makes it easy to add primer information and write it out to the
simple primer file format.
"""
def __init__(self):
self.primer_info = []
def __str__(self):
output = ""
for name, primer1, primer2 in self.primer_info:
output += "%s %s %s\n" % (name, primer1, primer2)
return output
def add_primer_set(self, primer_name, first_primer_seq,
second_primer_seq):
"""Add primer information to the record.
"""
self.primer_info.append((primer_name, first_primer_seq,
second_primer_seq))
class PrimerSearchParser:
"""Parse primersearch output into a PrimerSearchOutputRecord.
"""
def __init__(self, debug_level = 0):
self._scanner = _PrimerSearchScanner(debug_level)
def parse(self, handle):
self._consumer = _PrimerSearchRecordConsumer()
self._scanner.feed(handle, self._consumer)
return self._consumer.data
class PrimerSearchOutputRecord:
"""Represent the information from a primersearch job.
amplifiers is a dictionary where the keys are the primer names and
the values are a list of PrimerSearchAmplifier objects.
"""
def __init__(self):
self.amplifiers = {}
class PrimerSearchAmplifier:
"""Represent a single amplification from a primer.
"""
def __init__(self):
self.hit_info = ""
self.length = 0
class _PrimerSearchRecordConsumer(AbstractConsumer):
"""Get output from primersearch into a PrimerSearchOutputRecord
"""
def __init__(self):
self.data = PrimerSearchOutputRecord()
self._cur_primer = None
self._cur_amplifier = None
def _add_last_amplifier(self):
# add on the last amplifier
if self._cur_primer is not None and self._cur_amplifier is not None:
self.data.amplifiers[self._cur_primer].append(self._cur_amplifier)
def primer_name(self, name):
self._add_last_amplifier()
self.data.amplifiers[name] = []
self._cur_primer = name
def amplifier(self, amplifier_num):
self._add_last_amplifier()
self._cur_amplifier = PrimerSearchAmplifier()
def amplifier_sequence(self, sequence_info):
self._cur_amplifier.hit_info = sequence_info
def amplifier_length(self, amplifier_info):
self._cur_amplifier.length = int(amplifier_info)
def end_record(self):
self._add_last_amplifier()
class _PrimerSearchScanner:
"""Scan output from the primersearch program.
"""
def __init__(self, debug = 0):
self.interest_tags = ["primer_name", "amplifier",
"amplifier_sequence", "amplifier_length",
"end_record"]
expression = Martel.select_names(primersearch_format.record,
self.interest_tags)
self._parser = expression.make_parser(debug_level = debug)
def feed(self, handle, consumer):
self._parser.setContentHandler(EventGenerator(consumer,
self.interest_tags,
_strip_and_combine))
self._parser.setErrorHandler(handler.ErrorHandler())
self._parser.parseFile(handle)
consumer.end_record()
# --- primer3
class Primer3Record:
"""Represent information from a primer3 run finding primers.
Members:
primers A list of primers that are generated (usually 5)
"""
def __init__(self):
self.comments = ""
self.primers = []
class Primer3Primers:
"""A primer set designed by Primer3.
Members:
size
forward_seq
forward_start
forward_length
forward_tm
forward_gc
reverse_seq
reverse_start
reverse_length
reverse_tm
reverse_gc
"""
def __init__(self):
self.size = 0
self.forward_seq = ""
self.forward_start = 0
self.forward_length = 0
self.forward_tm = 0.0
self.forward_gc = 0.0
self.reverse_seq = ""
self.reverse_start = 0
self.reverse_length = 0
self.reverse_tm = 0.0
self.reverse_gc = 0.0
class Primer3Parser:
"""Parse primer3 output into a Primer3Record.
"""
def __init__(self, debug_level = 0):
self._scanner = _Primer3Scanner(debug_level)
def parse(self, handle):
self._consumer = _Primer3RecordConsumer()
self._scanner.feed(handle, self._consumer)
return self._consumer.data
class _Primer3RecordConsumer(AbstractConsumer):
"""Get output from prime3 into a Primer3Record
"""
def __init__(self):
self.data = Primer3Record()
self._cur_primer = None
def _add_last_primer(self):
# add on the last amplifier
if self._cur_primer is not None:
self.data.primers.append(self._cur_primer)
def comments(self, comment):
self.data.comments = comment
def start_primer(self, junk):
self._add_last_primer()
self._cur_primer = Primer3Primers()
def single_primer_line(self, junk):
self.start_primer(junk)
def product_size(self, size):
self._cur_primer.size = int(size)
def forward_start(self, start):
self._cur_primer.forward_start = int(start)
def forward_length(self, length):
self._cur_primer.forward_length = int(length)
def forward_tm(self, tm):
self._cur_primer.forward_tm = float(tm)
def forward_gc(self, gc):
self._cur_primer.forward_gc = float(gc)
def forward_seq(self, seq):
self._cur_primer.forward_seq = seq
def reverse_start(self, start):
self._cur_primer.reverse_start = int(start)
def reverse_length(self, length):
self._cur_primer.reverse_length = int(length)
def reverse_tm(self, tm):
self._cur_primer.reverse_tm = float(tm)
def reverse_gc(self, gc):
self._cur_primer.reverse_gc = float(gc)
def reverse_seq(self, seq):
self._cur_primer.reverse_seq = seq
def internal_start(self, start):
self._cur_primer.internal_start = int(start)
def internal_length(self, length):
self._cur_primer.internal_length = int(length)
def internal_tm(self, tm):
self._cur_primer.internal_tm = float(tm)
def internal_gc(self, gc):
self._cur_primer.internal_gc = float(gc)
def internal_seq(self, seq):
self._cur_primer.internal_seq = seq
def end_record(self):
self._add_last_primer()
class _Primer3Scanner:
"""Scan output from the primer3 program.
"""
def __init__(self, debug = 0):
self.interest_tags = ["comments", "single_primer_line",
"start_primer", "product_size",
"forward_start", "forward_length",
"forward_tm", "forward_gc", "forward_seq",
"reverse_start", "reverse_length",
"reverse_tm", "reverse_gc", "reverse_seq",
"internal_start", "internal_length",
"internal_tm", "internal_gc", "internal_seq",
"end_record"]
expression = Martel.select_names(primer3_format.record,
self.interest_tags)
self._parser = expression.make_parser(debug_level = debug)
def feed(self, handle, consumer):
self._parser.setContentHandler(EventGenerator(consumer,
self.interest_tags,
_strip_and_combine))
self._parser.setErrorHandler(handler.ErrorHandler())
self._parser.parseFile(handle)
consumer.end_record()
def _strip_and_combine(line_list):
"""Combine multiple lines of content separated by spaces.
"""
# first strip out extra whitespace
stripped_line_list = map(string.strip, line_list)
# now combine everything with spaces
return string.join(stripped_line_list, ' ')
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