From 40dfef179c73bfbe0b7f3bc848ad500c677f4a67 Mon Sep 17 00:00:00 2001
From: baer0006 <max.baer@unibas.ch>
Date: Wed, 16 Nov 2022 15:29:44 +0100
Subject: [PATCH] CreatePrimer class and preprocessing module
---
primingsitepredictor/Primer1.fasta | 2 ++
.../__pycache__/createprimer.cpython-39.pyc | Bin 0 -> 1156 bytes
primingsitepredictor/cli.py | 1 +
primingsitepredictor/createprimer.py | 27 ++++++++++++++++++
primingsitepredictor/preprocessingmodule.py | 21 ++++++++++++++
5 files changed, 51 insertions(+)
create mode 100644 primingsitepredictor/Primer1.fasta
create mode 100644 primingsitepredictor/__pycache__/createprimer.cpython-39.pyc
create mode 100644 primingsitepredictor/createprimer.py
create mode 100644 primingsitepredictor/preprocessingmodule.py
diff --git a/primingsitepredictor/Primer1.fasta b/primingsitepredictor/Primer1.fasta
new file mode 100644
index 0000000..545f110
--- /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
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diff --git a/primingsitepredictor/cli.py b/primingsitepredictor/cli.py
index 0dfcc2a..518fea1 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 0000000..c2c234f
--- /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 0000000..16b6da0
--- /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())
+
+
+
--
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