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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 | |