diff --git a/primingsitepredictor/Primer1.fasta b/primingsitepredictor/Primer1.fasta new file mode 100644 index 0000000000000000000000000000000000000000..545f1100114ec5eb992d22bc71d364b8663a7638 --- /dev/null +++ b/primingsitepredictor/Primer1.fasta @@ -0,0 +1,2 @@ +<primer1 +TTTTTTTTTTTTTTT diff --git a/primingsitepredictor/__pycache__/createprimer.cpython-39.pyc b/primingsitepredictor/__pycache__/createprimer.cpython-39.pyc new file mode 100644 index 0000000000000000000000000000000000000000..1ca66ef81e8844a5d2d6f5c892aba5f882018901 Binary files /dev/null and b/primingsitepredictor/__pycache__/createprimer.cpython-39.pyc differ diff --git a/primingsitepredictor/cli.py b/primingsitepredictor/cli.py index 0dfcc2a31990247eedeee0b4e712c9a8cde50229..518fea18a365aae2b8aa4eac5d264966adba984e 100644 --- a/primingsitepredictor/cli.py +++ b/primingsitepredictor/cli.py @@ -8,6 +8,7 @@ import argparse import logging def create_parser(): + """This function creates the parser""" parser = argparse.ArgumentParser( prog = 'Priming site predictor', description = 'Takes a cutoff energy and the predicts location of priming sites of transcripts', diff --git a/primingsitepredictor/createprimer.py b/primingsitepredictor/createprimer.py new file mode 100644 index 0000000000000000000000000000000000000000..c2c234f2eca3c07dd400098897f2586ceb0a7183 --- /dev/null +++ b/primingsitepredictor/createprimer.py @@ -0,0 +1,27 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Nov 16 14:17:06 2022 + +@author: baerma +""" + +class CreatePrimer: + """This Class creates an instance of a primer of a desired length and primer name + which can be saved as a fasta file. By default the length is 15 and name is primer1""" + def __init__(self, name='primer1', primerlength=15): + self.name = name + self.primer_length = primerlength + self.primer_sequence = 'T'*self.primer_length + self.lines = [f'<{self.name}', self.primer_sequence] + #print(self.primer) + #return self.primer + + def create_fasta(self): + with open(f'{self.name}.fasta', 'w') as f: + for line in self.lines: + f.write(line) + f.write('\n') + + + + diff --git a/primingsitepredictor/preprocessingmodule.py b/primingsitepredictor/preprocessingmodule.py new file mode 100644 index 0000000000000000000000000000000000000000..16b6da0f998d2b32183056b4959f6ce3657bcdf3 --- /dev/null +++ b/primingsitepredictor/preprocessingmodule.py @@ -0,0 +1,21 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Nov 16 14:17:06 2022 + +@author: baerma +""" +from createprimer import CreatePrimer + +def generate_RIBlast_input(): + """This function creates a list of the filenames for the RIBlast""" + my_primer = CreatePrimer() + my_primer.create_fasta() + primer_filename = my_primer.name +".fasta" + transcripts_filename = "transcripts.fasta" + + return [primer_filename, transcripts_filename] + +print(generate_RIBlast_input()) + + +