diff --git a/primingsitepredictor/createtranscript.py b/primingsitepredictor/createtranscript.py new file mode 100644 index 0000000000000000000000000000000000000000..9b114cc8b24521bd1806442522aa93d72517ce70 --- /dev/null +++ b/primingsitepredictor/createtranscript.py @@ -0,0 +1,38 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Nov 16 17:48:04 2022 + +@author: baerma +""" + +# with open("RIBlast output example.txt", 'r') as file: +# content = file.readlines() +# print(content[3:][0].strip(' \n').split(',')[-1].strip('()').split(':')) +# #create a instant of each transcript class +# print(len(content[3:])) +# print((content[3:])) + +class CreateTranscript(): + def __init__(self): + with open("RIBlast output example.txt", 'r') as file: + self.list_of_interactions = file.readlines()[3:] + + + + def generate_interaction_list(self): + interaction_list = [] + for i in range(0, (len(self.list_of_interactions)-1)): + current_interaction = self.list_of_interactions[i].strip(' \n').split(',') + #print(self.list_of_interactions[i].strip(' \n').split(',')) + interaction_list.append(current_interaction) + return interaction_list + + + +transcriptlist = CreateTranscript() +print(transcriptlist.generate_interaction_list()) + +#go from interaction list to transcript list? -no we will serve them a interaction list. + + # print(content[3:][0].strip(' \n').split(',')[-1].strip('()').split(':')) + diff --git a/primingsitepredictor/postprocessingmodule.py b/primingsitepredictor/postprocessingmodule.py index 88e72e9e40e704fca70a30bdda31d1bddf7618f5..b090f86263a6ca2b5a9cce7ed4a63231c94fd40b 100644 --- a/primingsitepredictor/postprocessingmodule.py +++ b/primingsitepredictor/postprocessingmodule.py @@ -4,11 +4,14 @@ Created on Wed Nov 16 16:47:20 2022 @author: baerma """ -import csv + with open("RIBlast output example.txt", 'r') as file: content = file.readlines() - print(content[3:][0]) + print(content[3:][0].strip(' \n').split(',')[-1].strip('()').split(':')) + #create a instant of each transcript class + + #os.chdir('C:/Users/baerma/Desktop/PhD-Local/Lectures/Programming for Life Sciences/priming-site-predictor/primingsitepredictor')