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|
| """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 |
|
|
