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# Copyright 2008 Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code to interact with the primersearch program from EMBOSS."""
class InputRecord:
"""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):
"""Initialize the class."""
self.primer_info = []
def __str__(self):
"""Summarize the primersearch input record as a string."""
output = ""
for name, primer1, primer2 in self.primer_info:
output += f"{name} {primer1} {primer2}\n"
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 OutputRecord:
"""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):
"""Initialize the class."""
self.amplifiers = {}
class Amplifier:
"""Represent a single amplification from a primer."""
def __init__(self):
"""Initialize the class."""
self.hit_info = ""
self.length = 0
def read(handle):
"""Get output from primersearch into a PrimerSearchOutputRecord."""
record = OutputRecord()
for line in handle:
if not line.strip():
continue
elif line.startswith("Primer name"):
name = line.split()[-1]
record.amplifiers[name] = []
elif line.startswith("Amplimer"):
amplifier = Amplifier()
record.amplifiers[name].append(amplifier)
elif line.startswith("\tSequence: "):
amplifier.hit_info = line.replace("\tSequence: ", "")
elif line.startswith("\tAmplimer length: "):
length = line.split()[-2]
amplifier.length = int(length)
else:
amplifier.hit_info += line
for name in record.amplifiers:
for amplifier in record.amplifiers[name]:
amplifier.hit_info = amplifier.hit_info.rstrip()
return record
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