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"""Code to interact with Primer-related programs from EMBOSS (DEPRECATED).
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Bio.Emboss.Primer has been deprecated, please use Bio.Emboss.Primer3 or
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Bio.Emboss.PrimerSearch instead.
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To parse primersearch output into a PrimerSearch.OutputRecord, use
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from Bio.Emboss import PrimerSearch
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handle = open('myprimersearchoutputfile.txt')
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record = PrimerSearch.read(handle)
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To parse primer3 output into a Primer3.Record, use
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from Bio.Emboss import Primer3
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handle = open('myprimer3outputfile.txt')
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record = Primer3.read(handle)
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Bio.Emboss.Primer has been deprecated.
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Please use Bio.Emboss.Primer3 or Bio.Emboss.PrimerSearch instead.
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To parse primersearch output into a PrimerSearch.OutputRecord, use
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from Bio.Emboss import PrimerSearch
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handle = open('myprimersearchoutputfile.txt')
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record = PrimerSearch.read(handle)
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To parse primer3 output into a Primer3.Record, use
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from Bio.Emboss import Primer3
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handle = open('myprimer3outputfile.txt')
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record = Primer3.read(handle)
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""", DeprecationWarning)
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from xml.sax import handler
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from Bio.ParserSupport import AbstractConsumer
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from Bio.ParserSupport import EventGenerator
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import primersearch_format
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class PrimerSearchInputRecord:
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"""Represent the input file into the primersearch program.
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This makes it easy to add primer information and write it out to the
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simple primer file format.
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for name, primer1, primer2 in self.primer_info:
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output += "%s %s %s\n" % (name, primer1, primer2)
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def add_primer_set(self, primer_name, first_primer_seq,
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"""Add primer information to the record.
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self.primer_info.append((primer_name, first_primer_seq,
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class PrimerSearchParser:
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"""Parse primersearch output into a PrimerSearchOutputRecord.
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def __init__(self, debug_level = 0):
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self._scanner = _PrimerSearchScanner(debug_level)
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def parse(self, handle):
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self._consumer = _PrimerSearchRecordConsumer()
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self._scanner.feed(handle, self._consumer)
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return self._consumer.data
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class PrimerSearchOutputRecord:
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"""Represent the information from a primersearch job.
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amplifiers is a dictionary where the keys are the primer names and
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the values are a list of PrimerSearchAmplifier objects.
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class PrimerSearchAmplifier:
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"""Represent a single amplification from a primer.
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class _PrimerSearchRecordConsumer(AbstractConsumer):
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"""Get output from primersearch into a PrimerSearchOutputRecord
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self.data = PrimerSearchOutputRecord()
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self._cur_primer = None
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self._cur_amplifier = None
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def _add_last_amplifier(self):
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# add on the last amplifier
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if self._cur_primer is not None and self._cur_amplifier is not None:
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self.data.amplifiers[self._cur_primer].append(self._cur_amplifier)
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def primer_name(self, name):
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self._add_last_amplifier()
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self.data.amplifiers[name] = []
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self._cur_primer = name
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def amplifier(self, amplifier_num):
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self._add_last_amplifier()
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self._cur_amplifier = PrimerSearchAmplifier()
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def amplifier_sequence(self, sequence_info):
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self._cur_amplifier.hit_info = sequence_info
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def amplifier_length(self, amplifier_info):
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self._cur_amplifier.length = int(amplifier_info)
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def end_record(self):
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self._add_last_amplifier()
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class _PrimerSearchScanner:
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"""Scan output from the primersearch program.
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def __init__(self, debug = 0):
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self.interest_tags = ["primer_name", "amplifier",
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"amplifier_sequence", "amplifier_length",
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expression = Martel.select_names(primersearch_format.record,
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self._parser = expression.make_parser(debug_level = debug)
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def feed(self, handle, consumer):
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self._parser.setContentHandler(EventGenerator(consumer,
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self._parser.setErrorHandler(handler.ErrorHandler())
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self._parser.parseFile(handle)
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consumer.end_record()
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"""Represent information from a primer3 run finding primers.
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primers A list of primers that are generated (usually 5)
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class Primer3Primers:
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"""A primer set designed by Primer3.
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self.forward_seq = ""
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self.forward_start = 0
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self.forward_length = 0
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self.forward_tm = 0.0
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self.forward_gc = 0.0
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self.reverse_seq = ""
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self.reverse_start = 0
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self.reverse_length = 0
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self.reverse_tm = 0.0
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self.reverse_gc = 0.0
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"""Parse primer3 output into a Primer3Record.
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def __init__(self, debug_level = 0):
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self._scanner = _Primer3Scanner(debug_level)
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def parse(self, handle):
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self._consumer = _Primer3RecordConsumer()
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self._scanner.feed(handle, self._consumer)
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return self._consumer.data
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class _Primer3RecordConsumer(AbstractConsumer):
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"""Get output from prime3 into a Primer3Record
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self.data = Primer3Record()
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self._cur_primer = None
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def _add_last_primer(self):
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# add on the last amplifier
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if self._cur_primer is not None:
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self.data.primers.append(self._cur_primer)
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def comments(self, comment):
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self.data.comments = comment
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def start_primer(self, junk):
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self._add_last_primer()
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self._cur_primer = Primer3Primers()
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def single_primer_line(self, junk):
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self.start_primer(junk)
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def product_size(self, size):
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self._cur_primer.size = int(size)
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def forward_start(self, start):
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self._cur_primer.forward_start = int(start)
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def forward_length(self, length):
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self._cur_primer.forward_length = int(length)
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def forward_tm(self, tm):
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self._cur_primer.forward_tm = float(tm)
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def forward_gc(self, gc):
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self._cur_primer.forward_gc = float(gc)
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def forward_seq(self, seq):
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self._cur_primer.forward_seq = seq
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def reverse_start(self, start):
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self._cur_primer.reverse_start = int(start)
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def reverse_length(self, length):
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self._cur_primer.reverse_length = int(length)
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def reverse_tm(self, tm):
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self._cur_primer.reverse_tm = float(tm)
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def reverse_gc(self, gc):
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self._cur_primer.reverse_gc = float(gc)
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def reverse_seq(self, seq):
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self._cur_primer.reverse_seq = seq
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def internal_start(self, start):
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self._cur_primer.internal_start = int(start)
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def internal_length(self, length):
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self._cur_primer.internal_length = int(length)
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def internal_tm(self, tm):
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self._cur_primer.internal_tm = float(tm)
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def internal_gc(self, gc):
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self._cur_primer.internal_gc = float(gc)
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def internal_seq(self, seq):
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self._cur_primer.internal_seq = seq
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def end_record(self):
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self._add_last_primer()
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class _Primer3Scanner:
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"""Scan output from the primer3 program.
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def __init__(self, debug = 0):
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self.interest_tags = ["comments", "single_primer_line",
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"start_primer", "product_size",
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"forward_start", "forward_length",
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"forward_tm", "forward_gc", "forward_seq",
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"reverse_start", "reverse_length",
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"reverse_tm", "reverse_gc", "reverse_seq",
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"internal_start", "internal_length",
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"internal_tm", "internal_gc", "internal_seq",
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expression = Martel.select_names(primer3_format.record,
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self._parser = expression.make_parser(debug_level = debug)
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def feed(self, handle, consumer):
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self._parser.setContentHandler(EventGenerator(consumer,
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self._parser.setErrorHandler(handler.ErrorHandler())
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self._parser.parseFile(handle)
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consumer.end_record()
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def _strip_and_combine(line_list):
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"""Combine multiple lines of content separated by spaces.
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# first strip out extra whitespace
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stripped_line_list = map(string.strip, line_list)
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# now combine everything with spaces
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return ' '.join(stripped_line_list)
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Bio/Emboss/Primer.py
