diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..bc0df40fcd50d8bd173ca9307fab0c095706e669
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,34 @@
+default: # Set default
+ tags:
+ - docker
+ image: python:3.10-slim-buster
+
+stages: # List of stages for jobs, and their order of execution
+ - build
+ - test
+
+build-job: # This job runs in the build stage, which runs first.
+ stage: build
+ script:
+ - pip install -r requirements.txt
+ - pip install -r requirements_dev.txt
+ - pip install .
+
+# unit-test-job: # This job runs in the test stage.
+# stage: test # It only starts when the job in the build stage completes successfully.
+# script:
+# - pip install -r requirements.txt
+# - pip install -r requirements_dev.txt
+# - pip install .
+# - coverage run --source primingsitepredictor -m pytest
+# - coverage report -m
+
+lint-test-job: # This job also runs in the test stage.
+ stage: test # It can run at the same time as unit-test-job (in parallel).
+ script:
+ - pip install -r requirements.txt
+ - pip install -r requirements_dev.txt
+ - pip install .
+ - flake8 --docstring-convention google primingsitepredictor/ # tests/
+ - pylint primingsitepredictor/ # tests/
+ - mypy primingsitepredictor/
diff --git a/img/Images_Max/Gitlesson_1_Max b/img/Images_Max/Gitlesson_1_Max
deleted file mode 100644
index abb7ab7d6243faab4be89850848c6b7b8f065488..0000000000000000000000000000000000000000
Binary files a/img/Images_Max/Gitlesson_1_Max and /dev/null differ
diff --git a/img/Images_Max/Gitlesson_2_Max b/img/Images_Max/Gitlesson_2_Max
deleted file mode 100644
index 8a36a512bb68851c3b48f3ebfd3b704600c62f8c..0000000000000000000000000000000000000000
Binary files a/img/Images_Max/Gitlesson_2_Max and /dev/null differ
diff --git a/img/Images_Max/Markdown_Max b/img/Images_Max/Markdown_Max
deleted file mode 100644
index 913791b6775544d80218e65551ca13c3add7b03d..0000000000000000000000000000000000000000
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diff --git a/img/Images_Max/images.txt b/img/Images_Max/images.txt
deleted file mode 100644
index 2571c8421ce9c8810dd41bba6aaed4237a0ef352..0000000000000000000000000000000000000000
--- a/img/Images_Max/images.txt
+++ /dev/null
@@ -1 +0,0 @@
-pepe
diff --git a/img/Images_Robin/IntroductionSeq.png b/img/Images_Robin/IntroductionSeq.png
deleted file mode 100644
index 968266787778e62890051b431de85ffd0168ad5a..0000000000000000000000000000000000000000
Binary files a/img/Images_Robin/IntroductionSeq.png and /dev/null differ
diff --git a/img/Images_Robin/Markdown.png b/img/Images_Robin/Markdown.png
deleted file mode 100644
index 6f2ba45ffd25e13860c830b358f3e047841b204a..0000000000000000000000000000000000000000
Binary files a/img/Images_Robin/Markdown.png and /dev/null differ
diff --git a/img/Images_Robin/Push&Pull -- GitRemotes!.png b/img/Images_Robin/Push&Pull -- GitRemotes!.png
deleted file mode 100644
index b5906235ab4d46cc5f75a16d0945ee05a2d9ff81..0000000000000000000000000000000000000000
Binary files a/img/Images_Robin/Push&Pull -- GitRemotes!.png and /dev/null differ
diff --git a/primingsitepredictor/.idea/.gitignore b/primingsitepredictor/.idea/.gitignore
deleted file mode 100644
index 13566b81b018ad684f3a35fee301741b2734c8f4..0000000000000000000000000000000000000000
--- a/primingsitepredictor/.idea/.gitignore
+++ /dev/null
@@ -1,8 +0,0 @@
-# Default ignored files
-/shelf/
-/workspace.xml
-# Editor-based HTTP Client requests
-/httpRequests/
-# Datasource local storage ignored files
-/dataSources/
-/dataSources.local.xml
diff --git a/primingsitepredictor/.idea/inspectionProfiles/profiles_settings.xml b/primingsitepredictor/.idea/inspectionProfiles/profiles_settings.xml
deleted file mode 100644
index 105ce2da2d6447d11dfe32bfb846c3d5b199fc99..0000000000000000000000000000000000000000
--- a/primingsitepredictor/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<component name="InspectionProjectProfileManager">
- <settings>
- <option name="USE_PROJECT_PROFILE" value="false" />
- <version value="1.0" />
- </settings>
-</component>
\ No newline at end of file
diff --git a/primingsitepredictor/.idea/misc.xml b/primingsitepredictor/.idea/misc.xml
deleted file mode 100644
index e6a7aa474cd32e70c4d9694c40996d01e47c23fc..0000000000000000000000000000000000000000
--- a/primingsitepredictor/.idea/misc.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.10 (tests)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/primingsitepredictor/.idea/modules.xml b/primingsitepredictor/.idea/modules.xml
deleted file mode 100644
index b7f52b9584a9cd9443097c0f753a17a344fa41a0..0000000000000000000000000000000000000000
--- a/primingsitepredictor/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectModuleManager">
- <modules>
- <module fileurl="file://$PROJECT_DIR$/.idea/primingsitepredictor.iml" filepath="$PROJECT_DIR$/.idea/primingsitepredictor.iml" />
- </modules>
- </component>
-</project>
\ No newline at end of file
diff --git a/primingsitepredictor/.idea/primingsitepredictor.iml b/primingsitepredictor/.idea/primingsitepredictor.iml
deleted file mode 100644
index d0876a78d06ac03b5d78c8dcdb95570281c6f1d6..0000000000000000000000000000000000000000
--- a/primingsitepredictor/.idea/primingsitepredictor.iml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
- <component name="NewModuleRootManager">
- <content url="file://$MODULE_DIR$" />
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- </component>
-</module>
\ No newline at end of file
diff --git a/primingsitepredictor/.idea/vcs.xml b/primingsitepredictor/.idea/vcs.xml
deleted file mode 100644
index 6c0b8635858dc7ad44b93df54b762707ce49eefc..0000000000000000000000000000000000000000
--- a/primingsitepredictor/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="VcsDirectoryMappings">
- <mapping directory="$PROJECT_DIR$/.." vcs="Git" />
- </component>
-</project>
\ No newline at end of file
diff --git a/primingsitepredictor/Primer1.fasta b/primingsitepredictor/Primer1.fasta
deleted file mode 100644
index 251777b9e4a409e7bb32d851b7bee98032bd3d6c..0000000000000000000000000000000000000000
--- a/primingsitepredictor/Primer1.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
-<primer1
-TTTTTTTTTTTTTTT
diff --git a/primingsitepredictor/__init__.py b/primingsitepredictor/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..66eb5ba958a8629efed8cbd53b8801505a0c219f 100644
--- a/primingsitepredictor/__init__.py
+++ b/primingsitepredictor/__init__.py
@@ -0,0 +1 @@
+"""Initialize package."""
diff --git a/primingsitepredictor/cli.py b/primingsitepredictor/cli.py
index 218fbb65b4c66ea098d317a17bbee015706d4933..3f5c9f791454ba8e0b82d5363460bfe24f92b67a 100644
--- a/primingsitepredictor/cli.py
+++ b/primingsitepredictor/cli.py
@@ -1,36 +1,115 @@
-# -*- coding: utf-8 -*-
-"""
-Changed on Fr Dec 23 16:49:50 2022
-
-@author: RobinC
-"""
+"""Receive command line arguments."""
import argparse
import logging
-import main
-
-class CLI():
- def create_parser(self):
- """This function creates the parser"""
-
- parser = argparse.ArgumentParser(
- prog = 'PrimingSitePredictor',
- description = 'Takes a cutoff energy and the predicts location of priming sites of transcripts',
- epilog = 'To predict or not to predict')
- parser.add_argument('--float', type=float, required=True, help='A energy-cutoff float number')
- parsed_args = parser.parse_args()
- energy_cutoff = parsed_args.float
- return energy_cutoff
-
- def letsgo(self):
- """This function creates a parser and prints the energycutoff"""
- energy_cutoff = CLI.create_parser()
- print(f"Your energy cutoff is {energy_cutoff}")
-
-if __name__ == '__main__':
+from primingsitepredictor.prime_site_predictor import CreatePrimer
+from primingsitepredictor.prime_site_predictor import PrimingSitePredictor
+
+LOG = logging.getLogger(__name__)
+
+
+def main():
+ """Use CLI arguments to predict priming sites."""
+ args = parse_args()
+ setup_logging()
+ LOG.info("Starting Priming Site Predictor...")
+
+ if args.primer_sequence is None:
+ primer = CreatePrimer().create_fasta()
+ args.primer_sequence = primer
+
+ predicted_sites = PrimingSitePredictor(
+ args.fasta_file, args.primer_sequence, args.energy_cutoff,
+ args.riblast_output, args.output_filename
+ )
+
+ predicted_sites.generate_gtf()
+
+ LOG.info("Priming Site Predictor finished.")
+
+
+def setup_logging() -> None:
+ """Configure logging.
+
+ Args:
+ verbosity: Level of logging verbosity.
+ """
logging.basicConfig(
- format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
+ format='[%(asctime)s: %(levelname)s] %(message)s \
+ (module "%(module)s")',
level=logging.INFO,
+ )
+
+
+def parse_args():
+ """Parse arguments for CLI."""
+ parser = argparse.ArgumentParser(
+ description="Compute potential priming sites using RIBlast."
+ )
+ parser.add_argument(
+ "-f", "--fasta-file",
+ help="Fasta-formatted file of transcript sequences"
+ )
+ parser.add_argument(
+ "-p", "--primer-sequence", default=None,
+ help="Primer sequence"
)
- LOG = logging.getLogger(__name__)
+ parser.add_argument(
+ "-e", "--energy-cutoff", type=float,
+ help="Energy cutoff for interactions"
+ )
+ parser.add_argument(
+ "-r", "--riblast-output",
+ help="Path to RIBlast output file"
+ )
+ parser.add_argument(
+ "-o", "--output-filename",
+ help="Path where the output gtf should be written"
+ )
+ args = parser.parse_args()
+
+ return args
+
+
+if __name__ == "__main__":
main()
+
+# def main():
+# """Execute generate_RIBlast."""
+# generate_riblast_input()
+
+
+# def generate_riblast_input():
+# """Create 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]
+
+
+# def create_gtf():
+# """Create gtf."""
+# gtf_file = PostProcessRIBlast().output
+# print(gtf_file)
+
+
+# def create_parser():
+# """Create a parser."""
+# parser = argparse.ArgumentParser(
+# prog='PrimingSitePredictor',
+# description='Takes a cutoff energy and the predicts \
+# location of priming sites of transcripts',
+# epilog='To predict or not to predict')
+# parser.add_argument('--float', type=float, required=True,
+# help='An energy-cutoff float number')
+# parsed_args = parser.parse_args()
+# energy_cutoff = parsed_args.float
+# return energy_cutoff
+
+
+# def letsgo():
+# """Create a parser and print the energycutoff."""
+# energy_cutoff = create_parser()
+# print(f"Your energy cutoff is {energy_cutoff}")
diff --git a/primingsitepredictor/createprimer.py b/primingsitepredictor/createprimer.py
deleted file mode 100644
index 8dcd2329f74f6f0c6254ff428dd323aa9bf8fe53..0000000000000000000000000000000000000000
--- a/primingsitepredictor/createprimer.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Changed on Fr Dec 23 14:34:20 2022
-
-@author: RobinC
-"""
-
-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]
-
-
- 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/main.py b/primingsitepredictor/main.py
deleted file mode 100644
index d8d80b1e26440880da3aaacd2ffa336ebe0a95cf..0000000000000000000000000000000000000000
--- a/primingsitepredictor/main.py
+++ /dev/null
@@ -1,30 +0,0 @@
-"""
-Changed on Tue Dec 20 14:06:20 2022
-
-@author: RobinC
-"""
-import sys
-from createprimer import CreatePrimer
-from postprocessing import PostProcessRIBlast
-
-
-def main():
- generate_RIBlast_input()
-
-
-
-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]
-
-def create_gtf():
- gtf_file = PostProcessRIBlast().output
- print(gtf_file)
-
-if __name__ == '__main__':
- main()
diff --git a/primingsitepredictor/my_primer.fasta b/primingsitepredictor/my_primer.fasta
deleted file mode 100644
index 70ef81c7f1201827c1886f6cf15efec0ec65ecf3..0000000000000000000000000000000000000000
--- a/primingsitepredictor/my_primer.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
-<my_primer
-TTTTTTTTTTTTTTTTTTTT
diff --git a/primingsitepredictor/output_transcripts_df.txt b/primingsitepredictor/output_transcripts_df.txt
deleted file mode 100644
index 89ba6f367701e787b727d3602c241853c88d61d8..0000000000000000000000000000000000000000
--- a/primingsitepredictor/output_transcripts_df.txt
+++ /dev/null
@@ -1,33 +0,0 @@
-Transcript_1 RIBlast Priming_site 2974 2988 . + . Interaction_Energy "0.01341899394212988"
-Transcript_1 RIBlast Priming_site 4 18 . + . Interaction_Energy "0.029617468622161858"
-Transcript_1 RIBlast Priming_site 3 17 . + . Interaction_Energy "0.033652793432239245"
-Transcript_1 RIBlast Priming_site 2 16 . + . Interaction_Energy "0.0436763978338453"
-Transcript_1 RIBlast Priming_site 1 15 . + . Interaction_Energy "0.07361927731913716"
-Transcript_1 RIBlast Priming_site 0 14 . + . Interaction_Energy "0.07913386517826602"
-Transcript_2 RIBlast Priming_site 1270 1284 . + . Interaction_Energy "0.023871738821072214"
-Transcript_2 RIBlast Priming_site 1269 1283 . + . Interaction_Energy "0.021998205780680843"
-Transcript_2 RIBlast Priming_site 1268 1282 . + . Interaction_Energy "0.02017380792576395"
-Transcript_2 RIBlast Priming_site 1267 1281 . + . Interaction_Energy "0.018400390375292373"
-Transcript_2 RIBlast Priming_site 1266 1280 . + . Interaction_Energy "0.016661952134191884"
-Transcript_2 RIBlast Priming_site 1265 1279 . + . Interaction_Energy "0.015028790572682043"
-Transcript_2 RIBlast Priming_site 1264 1278 . + . Interaction_Energy "0.013507972357530618"
-Transcript_2 RIBlast Priming_site 1263 1277 . + . Interaction_Energy "0.012121303370956734"
-Transcript_2 RIBlast Priming_site 1262 1276 . + . Interaction_Energy "0.0108940605154748"
-Transcript_2 RIBlast Priming_site 1261 1275 . + . Interaction_Energy "0.009818208415333858"
-Transcript_2 RIBlast Priming_site 1260 1274 . + . Interaction_Energy "0.008876574189642966"
-Transcript_2 RIBlast Priming_site 1259 1273 . + . Interaction_Energy "0.00807212607564225"
-Transcript_2 RIBlast Priming_site 1258 1272 . + . Interaction_Energy "0.007386053280385996"
-Transcript_2 RIBlast Priming_site 1257 1271 . + . Interaction_Energy "0.006777457533826199"
-Transcript_2 RIBlast Priming_site 1256 1270 . + . Interaction_Energy "0.006231339626935633"
-Transcript_2 RIBlast Priming_site 1255 1269 . + . Interaction_Energy "0.005701431631106869"
-Transcript_2 RIBlast Priming_site 1254 1268 . + . Interaction_Energy "0.005221962850186007"
-Transcript_2 RIBlast Priming_site 1253 1267 . + . Interaction_Energy "0.004743243630707861"
-Transcript_2 RIBlast Priming_site 1252 1266 . + . Interaction_Energy "0.0043514767009977685"
-Transcript_2 RIBlast Priming_site 1251 1265 . + . Interaction_Energy "0.004001246269203596"
-Transcript_2 RIBlast Priming_site 1250 1264 . + . Interaction_Energy "0.0035602658910861193"
-Transcript_2 RIBlast Priming_site 1249 1263 . + . Interaction_Energy "0.0034681706680775195"
-Transcript_2 RIBlast Priming_site 1248 1262 . + . Interaction_Energy "0.003588271464203091"
-Transcript_2 RIBlast Priming_site 1247 1261 . + . Interaction_Energy "0.0037963420302257692"
-Transcript_2 RIBlast Priming_site 1246 1260 . + . Interaction_Energy "0.004081499678888505"
-Transcript_2 RIBlast Priming_site 1245 1259 . + . Interaction_Energy "0.004411927146940477"
-Transcript_2 RIBlast Priming_site 1244 1258 . + . Interaction_Energy "0.00480978620121743"
diff --git a/primingsitepredictor/postprocessing.py b/primingsitepredictor/postprocessing.py
deleted file mode 100644
index e2504e0f98e7a6527f508715d018aace78066c5c..0000000000000000000000000000000000000000
--- a/primingsitepredictor/postprocessing.py
+++ /dev/null
@@ -1,69 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Tue Dec 20 14:06:20 2022
-
-@author: baerma
-"""
-
-import pandas as pd
-import math
-pd.options.mode.chained_assignment = None
-
-class PostProcessRIBlast():
-
- def __init__(self):
- output = self.generate_gtf()
- #print(output)
-
-
- def calculate_energy(self, value):
- energy_constant = 1.380649*10**(-23)*298
- kcalmol_joul = 6.9477*10**-21
- return (math.exp(-float(value)*kcalmol_joul/energy_constant))
-
-
- def create_list_from_output(self):
- self.file = "RIBlast output example.txt"
- self.firstline = 3
- self.interaction_list = []
- with open(self.file, 'r') as file:
- self.raw_interactions = file.readlines()[self.firstline:]
- self.number_entries = len(self.raw_interactions)
-
- for i in range(0, self.number_entries-1):
- current_interaction = self.raw_interactions[i].strip(' \n').replace('(', '').replace(')','').replace('-',',').replace(':',',').split(',')
- self.interaction_list.append(current_interaction)
-
- return self.interaction_list
-
-
- def create_pandas_df(self):
- self.interaction_list = self.create_list_from_output()
- self.df = pd.DataFrame(self.interaction_list)
- self.df['Number_of_interactions'] = int(0)
- self.df['Interaction_Energy'] = float(0)
- self.transcript = 3
- self.energy = 5
-
- for index in self.df.index:
- self.df['Number_of_interactions'][index]=self.df[self.transcript].value_counts()[self.df[self.transcript][index]]
- self.df['Interaction_Energy'][index]=self.calculate_energy(self.df[self.energy][index])
-
- self.df['Normalised_interaction_energy']=self.df['Interaction_Energy']/self.df['Number_of_interactions']
-
- return self.df
-
-
- def generate_gtf(self):
- self.interaction_df = self.create_pandas_df()
- self.output = str()
-
- for index in self.interaction_df.index:
- self.output = self.output + str(self.interaction_df[3][index]+'\t' + 'RIBlast' + '\t' + 'Priming_site' + '\t' + self.interaction_df[13][index] + '\t' + self.interaction_df[12][index] + '\t' + '.' + '\t' + '+' + '\t' + '.' + '\t' + f'Interaction_Energy "{self.interaction_df["Normalised_interaction_energy"][index]}"' + '\n')
-
- with open('output_transcripts_df.GTF', 'w') as f:
- f.write(self.output)
- return(self.output)
-
-
-print(PostProcessRIBlast().output)
\ No newline at end of file
diff --git a/primingsitepredictor/prime_site_predictor.py b/primingsitepredictor/prime_site_predictor.py
new file mode 100644
index 0000000000000000000000000000000000000000..bbc3cd31e1ca2ab7eeb7e05e23beb94658b7acc0
--- /dev/null
+++ b/primingsitepredictor/prime_site_predictor.py
@@ -0,0 +1,119 @@
+"""Main module for Priming Site Predictor."""
+import math
+import logging
+import pandas as pd # type: ignore
+
+LOG = logging.getLogger(__name__)
+
+
+# pylint: disable=R0903
+class CreatePrimer:
+ """Create 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 primer.
+ """
+
+ def __init__(self, name='primer', primerlength=15):
+ """Initiate function."""
+ self.name = name
+ self.primer_length = primerlength
+ self.primer_sequence = 'T'*self.primer_length
+ self.lines = [f'<{self.name}', self.primer_sequence]
+
+ def create_fasta(self):
+ """Create primer fasta file."""
+ primer = self.lines
+ LOG.info("Created primer.")
+ with open(f'{self.name}.fasta', 'w', encoding="utf-8") as file:
+ file.write('\n'.join(self.lines))
+ return primer
+
+
+# pylint: disable=R0913
+class PrimingSitePredictor:
+ """Generate primer sites based on RIBlast results."""
+
+ # pylint: disable=R0913
+ def __init__(
+ self, fasta_file, primer_sequence, energy_cutoff,
+ riblast_output, output_filename
+ ):
+ """Initiate."""
+ self.fasta_file = fasta_file
+ self.primer_sequence = primer_sequence
+ self.energy_cutoff = energy_cutoff
+ self.riblast_output = riblast_output
+ self.output_filename = output_filename
+
+ def calculate_energy(self, value):
+ """Calculate hybridization energy."""
+ energy_constant = 1.380649e-23*298
+ kcalmol_joul = 6.9477*10**-21
+ return (math.exp(-float(value)*kcalmol_joul/energy_constant))
+
+ def create_list_from_output(self):
+ """Create list from output."""
+ firstline = 3
+ interaction_list = []
+ with open(self.riblast_output, 'r', encoding="utf-8") as file:
+ raw_interactions = file.readlines()[firstline:]
+ number_entries = len(raw_interactions)
+
+ for i in range(0, number_entries-1):
+ current_interaction = raw_interactions[i].strip(
+ ' \n').replace('(', '').replace(')', '').replace(
+ '-', ',').replace(':', ',').split(',')
+ interaction_list.append(current_interaction)
+
+ return interaction_list
+
+ def create_pandas_df(self):
+ """Create interaction df."""
+ interaction_list = self.create_list_from_output()
+ interaction_df = pd.DataFrame(interaction_list)
+ interaction_df['Number_of_interactions'] = int(0)
+ interaction_df['Interaction_Energy'] = float(0)
+ transcript = 3
+ energy = 5
+
+ for _ in interaction_df.index:
+ interaction_df['Number_of_interactions'] = interaction_df[
+ transcript
+ ].apply(
+ lambda x: interaction_df[transcript].value_counts()[x]
+ )
+ interaction_df['Interaction_Energy'] = interaction_df[
+ energy
+ ].apply(self.calculate_energy)
+
+ LOG.info("Calculating normalised interaction energies...")
+ interaction_df['Normalised_interaction_energy'] = interaction_df[
+ 'Interaction_Energy']/interaction_df['Number_of_interactions']
+
+ return interaction_df
+
+ def generate_gtf(self):
+ """Generate gtf file."""
+ interaction_df = self.create_pandas_df()
+ result = str()
+
+ for index in interaction_df.index:
+ result += (
+ str(interaction_df[3][index])
+ + '\tRIBlast\tPriming_site\t'
+ + str(interaction_df[13][index])
+ + '\t'
+ + str(interaction_df[12][index])
+ + '\t.\t+\t.\t'
+ + 'Interaction_Energy' + '\t'
+ + str(interaction_df[
+ "Normalised_interaction_energy"
+ ][index])
+ + '\n'
+ )
+
+ LOG.info("Generating output gtf file...")
+ with open(self.output_filename, 'w', encoding="utf-8") as file:
+ file.write(result)
+ return result
diff --git a/primingsitepredictor/test/RIBlast output example.txt b/primingsitepredictor/test/RIBlast output example.txt
deleted file mode 100644
index f3a270893926da9f8b302af5b15dbed875a6475f..0000000000000000000000000000000000000000
--- a/primingsitepredictor/test/RIBlast output example.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-RIblast ris result
-input:queryRNA.fa,database:test_db,RepeatFlag:0,MaximalSpan:70,MinAccessibleLength:5,MaxSeedLength:20,InteractionEnergyThreshold:-4,HybridEnergyThreshold:-6,FinalThreshold:-8,DropOutLengthWoGap:5,DropOutLengthWGap:16
-Id,Query name, Query Length, Target name, Target Length, Accessibility Energy, Hybridization Energy, Interaction Energy, BasePair
-0,Test_Primer,15,Transcript_1,3233,1.49191,-9.76,-8.26809,(0-14:2988-2974)
-1,Test_Primer,15,Transcript_1,3233,1.02308,-9.76,-8.73692,(0-14:18-4)
-2,Test_Primer,15,Transcript_1,3233,0.947439,-9.73,-8.78256,(0-14:17-3)
-3,Test_Primer,15,Transcript_1,3233,0.793049,-9.73,-8.93695,(0-14:16-2)
-4,Test_Primer,15,Transcript_1,3233,0.483869,-9.73,-9.24613,(0-14:15-1)
-5,Test_Primer,15,Transcript_1,3233,0.441093,-9.17,-8.72891,(0-14:14-0)
-6,Test_Primer,15,Transcript_2,1285,0.260102,-9.1,-8.8399,(0-14:1284-1270)
-7,Test_Primer,15,Transcript_2,1285,0.308504,-9.73,-9.4215,(0-14:1283-1269)
-8,Test_Primer,15,Transcript_2,1285,0.359773,-9.73,-9.37023,(0-14:1282-1268)
-9,Test_Primer,15,Transcript_2,1285,0.414262,-9.73,-9.31574,(0-14:1281-1267)
-10,Test_Primer,15,Transcript_2,1285,0.473033,-9.73,-9.25697,(0-14:1280-1266)
-11,Test_Primer,15,Transcript_2,1285,0.534123,-9.73,-9.19588,(0-14:1279-1265)
-12,Test_Primer,15,Transcript_2,1285,0.597302,-9.73,-9.1327,(0-14:1278-1264)
-13,Test_Primer,15,Transcript_2,1285,0.661445,-9.73,-9.06855,(0-14:1277-1263)
-14,Test_Primer,15,Transcript_2,1285,0.724659,-9.73,-9.00534,(0-14:1276-1262)
-15,Test_Primer,15,Transcript_2,1285,0.786234,-9.73,-8.94377,(0-14:1275-1261)
-16,Test_Primer,15,Transcript_2,1285,0.84594,-9.73,-8.88406,(0-14:1274-1260)
-17,Test_Primer,15,Transcript_2,1285,0.902197,-9.73,-8.8278,(0-14:1273-1259)
-18,Test_Primer,15,Transcript_2,1285,0.954797,-9.73,-8.7752,(0-14:1272-1258)
-19,Test_Primer,15,Transcript_2,1285,1.00572,-9.73,-8.72428,(0-14:1271-1257)
-20,Test_Primer,15,Transcript_2,1285,1.05547,-9.73,-8.67453,(0-14:1270-1256)
-21,Test_Primer,15,Transcript_2,1285,1.1081,-9.73,-8.6219,(0-14:1269-1255)
-22,Test_Primer,15,Transcript_2,1285,1.16012,-9.73,-8.56988,(0-14:1268-1254)
-23,Test_Primer,15,Transcript_2,1285,1.21706,-9.73,-8.51294,(0-14:1267-1253)
-24,Test_Primer,15,Transcript_2,1285,1.26811,-9.73,-8.46189,(0-14:1266-1252)
-25,Test_Primer,15,Transcript_2,1285,1.3178,-9.73,-8.4122,(0-14:1265-1251)
-26,Test_Primer,15,Transcript_2,1285,1.38695,-9.73,-8.34305,(0-14:1264-1250)
-27,Test_Primer,15,Transcript_2,1285,1.40247,-9.73,-8.32753,(0-14:1263-1249)
-28,Test_Primer,15,Transcript_2,1285,1.38231,-9.73,-8.34769,(0-14:1262-1248)
-29,Test_Primer,15,Transcript_2,1285,1.34893,-9.73,-8.38107,(0-14:1261-1247)
-30,Test_Primer,15,Transcript_2,1285,1.30604,-9.73,-8.42396,(0-14:1260-1246)
-31,Test_Primer,15,Transcript_2,1285,1.25994,-9.73,-8.47006,(0-14:1259-1245)
-32,Test_Primer,15,Transcript_2,1285,1.20881,-9.76,-8.55119,(0-14:1258-1244)
-33,Test_Primer,15,Transcript_2,1285,1.63873,-9.91,-8.27127,(0-14:674-660)
diff --git a/primingsitepredictor/test/__init__.py b/primingsitepredictor/test/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/primingsitepredictor/test/output_transcripts_df.GTF b/primingsitepredictor/test/output_transcripts_df.GTF
deleted file mode 100644
index 89ba6f367701e787b727d3602c241853c88d61d8..0000000000000000000000000000000000000000
--- a/primingsitepredictor/test/output_transcripts_df.GTF
+++ /dev/null
@@ -1,33 +0,0 @@
-Transcript_1 RIBlast Priming_site 2974 2988 . + . Interaction_Energy "0.01341899394212988"
-Transcript_1 RIBlast Priming_site 4 18 . + . Interaction_Energy "0.029617468622161858"
-Transcript_1 RIBlast Priming_site 3 17 . + . Interaction_Energy "0.033652793432239245"
-Transcript_1 RIBlast Priming_site 2 16 . + . Interaction_Energy "0.0436763978338453"
-Transcript_1 RIBlast Priming_site 1 15 . + . Interaction_Energy "0.07361927731913716"
-Transcript_1 RIBlast Priming_site 0 14 . + . Interaction_Energy "0.07913386517826602"
-Transcript_2 RIBlast Priming_site 1270 1284 . + . Interaction_Energy "0.023871738821072214"
-Transcript_2 RIBlast Priming_site 1269 1283 . + . Interaction_Energy "0.021998205780680843"
-Transcript_2 RIBlast Priming_site 1268 1282 . + . Interaction_Energy "0.02017380792576395"
-Transcript_2 RIBlast Priming_site 1267 1281 . + . Interaction_Energy "0.018400390375292373"
-Transcript_2 RIBlast Priming_site 1266 1280 . + . Interaction_Energy "0.016661952134191884"
-Transcript_2 RIBlast Priming_site 1265 1279 . + . Interaction_Energy "0.015028790572682043"
-Transcript_2 RIBlast Priming_site 1264 1278 . + . Interaction_Energy "0.013507972357530618"
-Transcript_2 RIBlast Priming_site 1263 1277 . + . Interaction_Energy "0.012121303370956734"
-Transcript_2 RIBlast Priming_site 1262 1276 . + . Interaction_Energy "0.0108940605154748"
-Transcript_2 RIBlast Priming_site 1261 1275 . + . Interaction_Energy "0.009818208415333858"
-Transcript_2 RIBlast Priming_site 1260 1274 . + . Interaction_Energy "0.008876574189642966"
-Transcript_2 RIBlast Priming_site 1259 1273 . + . Interaction_Energy "0.00807212607564225"
-Transcript_2 RIBlast Priming_site 1258 1272 . + . Interaction_Energy "0.007386053280385996"
-Transcript_2 RIBlast Priming_site 1257 1271 . + . Interaction_Energy "0.006777457533826199"
-Transcript_2 RIBlast Priming_site 1256 1270 . + . Interaction_Energy "0.006231339626935633"
-Transcript_2 RIBlast Priming_site 1255 1269 . + . Interaction_Energy "0.005701431631106869"
-Transcript_2 RIBlast Priming_site 1254 1268 . + . Interaction_Energy "0.005221962850186007"
-Transcript_2 RIBlast Priming_site 1253 1267 . + . Interaction_Energy "0.004743243630707861"
-Transcript_2 RIBlast Priming_site 1252 1266 . + . Interaction_Energy "0.0043514767009977685"
-Transcript_2 RIBlast Priming_site 1251 1265 . + . Interaction_Energy "0.004001246269203596"
-Transcript_2 RIBlast Priming_site 1250 1264 . + . Interaction_Energy "0.0035602658910861193"
-Transcript_2 RIBlast Priming_site 1249 1263 . + . Interaction_Energy "0.0034681706680775195"
-Transcript_2 RIBlast Priming_site 1248 1262 . + . Interaction_Energy "0.003588271464203091"
-Transcript_2 RIBlast Priming_site 1247 1261 . + . Interaction_Energy "0.0037963420302257692"
-Transcript_2 RIBlast Priming_site 1246 1260 . + . Interaction_Energy "0.004081499678888505"
-Transcript_2 RIBlast Priming_site 1245 1259 . + . Interaction_Energy "0.004411927146940477"
-Transcript_2 RIBlast Priming_site 1244 1258 . + . Interaction_Energy "0.00480978620121743"
diff --git a/primingsitepredictor/test/output_transcripts_df.txt b/primingsitepredictor/test/output_transcripts_df.txt
deleted file mode 100644
index 89ba6f367701e787b727d3602c241853c88d61d8..0000000000000000000000000000000000000000
--- a/primingsitepredictor/test/output_transcripts_df.txt
+++ /dev/null
@@ -1,33 +0,0 @@
-Transcript_1 RIBlast Priming_site 2974 2988 . + . Interaction_Energy "0.01341899394212988"
-Transcript_1 RIBlast Priming_site 4 18 . + . Interaction_Energy "0.029617468622161858"
-Transcript_1 RIBlast Priming_site 3 17 . + . Interaction_Energy "0.033652793432239245"
-Transcript_1 RIBlast Priming_site 2 16 . + . Interaction_Energy "0.0436763978338453"
-Transcript_1 RIBlast Priming_site 1 15 . + . Interaction_Energy "0.07361927731913716"
-Transcript_1 RIBlast Priming_site 0 14 . + . Interaction_Energy "0.07913386517826602"
-Transcript_2 RIBlast Priming_site 1270 1284 . + . Interaction_Energy "0.023871738821072214"
-Transcript_2 RIBlast Priming_site 1269 1283 . + . Interaction_Energy "0.021998205780680843"
-Transcript_2 RIBlast Priming_site 1268 1282 . + . Interaction_Energy "0.02017380792576395"
-Transcript_2 RIBlast Priming_site 1267 1281 . + . Interaction_Energy "0.018400390375292373"
-Transcript_2 RIBlast Priming_site 1266 1280 . + . Interaction_Energy "0.016661952134191884"
-Transcript_2 RIBlast Priming_site 1265 1279 . + . Interaction_Energy "0.015028790572682043"
-Transcript_2 RIBlast Priming_site 1264 1278 . + . Interaction_Energy "0.013507972357530618"
-Transcript_2 RIBlast Priming_site 1263 1277 . + . Interaction_Energy "0.012121303370956734"
-Transcript_2 RIBlast Priming_site 1262 1276 . + . Interaction_Energy "0.0108940605154748"
-Transcript_2 RIBlast Priming_site 1261 1275 . + . Interaction_Energy "0.009818208415333858"
-Transcript_2 RIBlast Priming_site 1260 1274 . + . Interaction_Energy "0.008876574189642966"
-Transcript_2 RIBlast Priming_site 1259 1273 . + . Interaction_Energy "0.00807212607564225"
-Transcript_2 RIBlast Priming_site 1258 1272 . + . Interaction_Energy "0.007386053280385996"
-Transcript_2 RIBlast Priming_site 1257 1271 . + . Interaction_Energy "0.006777457533826199"
-Transcript_2 RIBlast Priming_site 1256 1270 . + . Interaction_Energy "0.006231339626935633"
-Transcript_2 RIBlast Priming_site 1255 1269 . + . Interaction_Energy "0.005701431631106869"
-Transcript_2 RIBlast Priming_site 1254 1268 . + . Interaction_Energy "0.005221962850186007"
-Transcript_2 RIBlast Priming_site 1253 1267 . + . Interaction_Energy "0.004743243630707861"
-Transcript_2 RIBlast Priming_site 1252 1266 . + . Interaction_Energy "0.0043514767009977685"
-Transcript_2 RIBlast Priming_site 1251 1265 . + . Interaction_Energy "0.004001246269203596"
-Transcript_2 RIBlast Priming_site 1250 1264 . + . Interaction_Energy "0.0035602658910861193"
-Transcript_2 RIBlast Priming_site 1249 1263 . + . Interaction_Energy "0.0034681706680775195"
-Transcript_2 RIBlast Priming_site 1248 1262 . + . Interaction_Energy "0.003588271464203091"
-Transcript_2 RIBlast Priming_site 1247 1261 . + . Interaction_Energy "0.0037963420302257692"
-Transcript_2 RIBlast Priming_site 1246 1260 . + . Interaction_Energy "0.004081499678888505"
-Transcript_2 RIBlast Priming_site 1245 1259 . + . Interaction_Energy "0.004411927146940477"
-Transcript_2 RIBlast Priming_site 1244 1258 . + . Interaction_Energy "0.00480978620121743"
diff --git a/primingsitepredictor/test/test_cli.py b/primingsitepredictor/test/test_cli.py
deleted file mode 100644
index dec66a1765914a96fbb354b33bcbbd07694833a7..0000000000000000000000000000000000000000
--- a/primingsitepredictor/test/test_cli.py
+++ /dev/null
@@ -1,103 +0,0 @@
-"""
-Created on Tue Dec 20 14:06:20 2022
-
-@author: RobinC
-"""
-
-# Imports
-import os, sys
-import pytest
-currentdir = os.path.dirname(os.path.realpath(__file__))
-parentdir = os.path.dirname(currentdir)
-sys.path.append(parentdir)
-import createprimer as cp
-import unittest
-import cli
-import argparse
-import pytest
-from unittest.mock import patch
-from unittest.mock import Mock
-import io
-import sys
-
-class TestCli(unittest.TestCase):
-
- def test_import(self):
- """Test function for module imports"""
- try:
- import argparse
- except ImportError:
- self.fail("Failed to import argparse")
-
- try:
- import logging
- except ImportError:
- self.fail("Failed to import logging")
-
- try:
- import main
- except ImportError:
- self.fail("Failed to import main")
-
-
-
- def test_create_parser(self):
-
- # Test parsing a float number
- float_num = 3.14
- float_str = str(float_num)
- self.assertEqual(float_num, cli.CLI.create_parser(['--float', float_str]))
-
- # Test parsing a float number with leading and trailing whitespace
- float_num = 3.14
- float_str = " " + str(float_num) + " "
- self.assertEqual(float_num, cli.CLI.create_parser(['--float', float_str]))
-
- # Test parsing a float number with a decimal point and no digits after it
- float_num = 3.
- float_str = str(float_num)
- self.assertEqual(float_num, cli.CLI.create_parser(['--float', float_str]))
-
- # Test parsing a float number with a decimal point and multiple digits after it
- float_num = 3.14159
- float_str = str(float_num)
- self.assertEqual(float_num, cli.CLI.create_parser(['--float', float_str]))
-
- # Test parsing a negative float number
- float_num = -3.14
- float_str = str(float_num)
- self.assertEqual(float_num, cli.CLI.create_parser(['--float', float_str]))
-
- def test_invalid_create_parser(self):
-
- # Test parsing a float number with a letter in it
- args = ['--float', '3.14a']
- with self.assertRaises(SystemExit):
- cli.CLI.create_parser(args)
-
- # Test parsing a float number with multiple decimal points
- args = ['--float', '3.14.159']
- with self.assertRaises(SystemExit):
- cli.CLI.create_parser(args)
-
- def test_letsgo(self):
-
- # Test printing a float number
- float_num = 3.14
- float_str = str(float_num)
- with self.assertLogs('', level='INFO') as cm:
- cli.CLI.letsgo(['--float', float_str])
- self.assertEqual(cm.output, [f'INFO:root:Your energy cutoff is {float_num}'])
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/primingsitepredictor/test/test_createprimer.py b/primingsitepredictor/test/test_createprimer.py
deleted file mode 100644
index a54ad9c01245b741d89346851b1b3a7c76ff726d..0000000000000000000000000000000000000000
--- a/primingsitepredictor/test/test_createprimer.py
+++ /dev/null
@@ -1,71 +0,0 @@
-"""
-Created on Tue Dec 20 14:06:20 2022
-
-@author: RobinC
-"""
-
-import os, sys
-import pytest
-currentdir = os.path.dirname(os.path.realpath(__file__))
-parentdir = os.path.dirname(currentdir)
-sys.path.append(parentdir)
-import createprimer as cp
-import unittest
-
-
-class TestCreatePrimer(unittest.TestCase):
-
- def test_init(self):
- """Test function for the __init__() method"""
-
- # Test default values
- primer = cp.CreatePrimer()
- self.assertEqual(primer.name, 'primer1')
- self.assertEqual(primer.primer_length, 15)
- self.assertEqual(primer.primer_sequence, 'T'*15)
- self.assertEqual(primer.lines, ['<primer1', 'TTTTTTTTTTTTTTT'])
-
- # Test custom values
- primer = cp.CreatePrimer('my_primer', 20)
- self.assertEqual(primer.name, 'my_primer')
- self.assertEqual(primer.primer_length, 20)
- self.assertEqual(primer.primer_sequence, 'T'*20)
- self.assertEqual(primer.lines, ['<my_primer', 'TTTTTTTTTTTTTTTTTTTT'])
-
-
- def test_create_fasta(self):
- """Test function for the test_create_fasta() method"""
-
- # Test default values
- primer = cp.CreatePrimer()
- primer.create_fasta()
- with open('primer1.fasta', 'r') as f:
- lines = f.readlines()
- self.assertEqual(lines, ['<primer1\n', 'TTTTTTTTTTTTTTT\n'])
-
- # Test custom values
- primer = cp.CreatePrimer('my_primer', 20)
- primer.create_fasta()
- with open('my_primer.fasta', 'r') as f:
- lines = f.readlines()
- self.assertEqual(lines, ['<my_primer\n', 'TTTTTTTTTTTTTTTTTTTT\n'])
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/primingsitepredictor/test/test_postprocessing.py b/primingsitepredictor/test/test_postprocessing.py
deleted file mode 100644
index 2948ef269fe44e369cd619e63ab930608e03dc8e..0000000000000000000000000000000000000000
--- a/primingsitepredictor/test/test_postprocessing.py
+++ /dev/null
@@ -1,157 +0,0 @@
-"""
-Created on Tue Dec 20 14:06:20 2022
-
-@author: RobinC
-"""
-
-# Imports
-import os, sys
-import pytest
-
-currentdir = os.path.dirname(os.path.realpath(__file__))
-parentdir = os.path.dirname(currentdir)
-sys.path.append(parentdir)
-import postprocessing as pp
-import unittest
-import math
-from unittest import mock
-
-
-class TestPostProcessRIBlast(unittest.TestCase):
- def test_import(self):
- """Test function for module imports"""
- try:
- import pandas
- except ImportError:
- self.fail("Failed to import pandas")
-
- try:
- import math
- except ImportError:
- self.fail("Failed to import math")
-
- def setUp(self):
- """Setup function to create an instance of PostProcessRIBlast()"""
-
- self.post_processor = pp.PostProcessRIBlast()
-
- def test_init(self):
- """Test function for the __init__() method"""
-
- # Test if generate_gtf method is being called
- with unittest.mock.patch.object(
- pp.PostProcessRIBlast, "generate_gtf"
- ) as mock_generate_gtf:
- pp.PostProcessRIBlast()
- mock_generate_gtf.assert_called_once()
-
- # Test if generate_gtf returns the expected output
- expected_output = (
- 'Transcript_1\tRIBlast\tPriming_site\t2974[3257 chars]3"\n'
- )
- self.assertEqual(self.post_processor.generate_gtf(), expected_output)
-
- def test_calculate_energy(self):
- """Test function for the calculate_energy() method"""
-
- def calculate_energy(value):
- energy_constant = 1.380649*10**(-23)*298
- kcalmol_joul = 6.9477*10**-21
- return (math.exp(-float(value)*kcalmol_joul/energy_constant))
-
- # set a decimal place
- decimalPlace = 20
-
- # Test for a positive value
- self.testinstance = pp.PostProcessRIBlast.calculate_energy(self, 5.0)
- expected_output = calculate_energy(5.0)
- self.assertAlmostEqual(self.testinstance, expected_output, decimalPlace)
-
-
- # Test for a negative value
- self.testinstance = pp.PostProcessRIBlast.calculate_energy(self, -5.0)
- expected_output = calculate_energy(-5.0)
- self.assertAlmostEqual(self.testinstance, expected_output, decimalPlace)
-
- # Test for zero
- self.testinstance = pp.PostProcessRIBlast.calculate_energy(self, 0)
- expected_output = calculate_energy(0)
- self.assertAlmostEqual(self.testinstance, expected_output, decimalPlace)
-
-
- def test_create_list_from_output(self):
- """Test function for the create_list_from_output() method"""
-
- #create an instance test of the class PostProcessRIBlast()
- test = pp.PostProcessRIBlast()
- test.file = "RIBlast output example.txt"
-
- with open('RIBlast output example.txt', 'r') as file:
- data_list = file.readlines()
-
- # Remove the header
- data_list = data_list[3:]
-
- # Convert each row of the list into a list of values
- expected_output = []
- for row in data_list:
- # Split the row by the comma character
- values = row.strip().split(',')
- # Append the list of values to the final list
- expected_output.append(values)
- return expected_output
- self.assertEqual(test.create_list_from_output(), expected_output)
-
-
- def test_create_pandas_df(self):
- """Test function for the create_pandas_df() method with mock data"""
-
- # create a test instance
- test_instance = pp.PostProcessRIBlast()
-
- # create some mock data for the input list
- test_instance.interaction_list= [
- ['Id','Query name', 'Query Length', 'Target name', 'Target Length', 'Accessibility Energy', 'Hybridization Energy', 'Interaction Energy', 'BasePair'],
- [0,'Test_Primer',15,'Transcript_1',3233,1.49191,-9.76,-8.26809,'(0-14:2988-2974)'],
- [1,'Test_Primer',15,'Transcript_1',3233,1.02308,-9.76,-8.73692,'(0-14:18-4)'],
- [2,'Test_Primer',15,'Transcript_1',3233,0.947439,-9.73,-8.78256,'(0-14:17-3)'],
- [3,'Test_Primer',15,'Transcript_1',3233,0.793049,-9.73,-8.93695,'(0-14:16-2)'],
- [4,'Test_Primer',15,'Transcript_1',3233,0.483869,-9.73,-9.24613,'(0-14:15-1)'],
- [5,'Test_Primer',15,'Transcript_1',3233,0.441093,-9.17,-8.72891,'(0-14:14-0)']]
-
- # create the DataFrame using the mock data
- df = test_instance.create_pandas_df()
-
- #self.assertEqual(len(df),7)
-
- # check that the DataFrame has the expected column names
- #self.assertEqual(list(df.columns), ['Id','Query name', 'Query Length', 'Target name', 'Target Length', 'Accessibility Energy', 'Hybridization Energy', 'Interaction Energy', 'BasePair'])
-
- # check that the values in the 'Id' column are correct
- self.assertEqual(list(df['Id']), ['Id',0,1,2,3,4,5])
-
- # check that the values in the 'Query name' column are correct
- self.assertEqual(list(df['Query name']), ['Query name','Test_Primer','Test_Primer','Test_Primer','Test_Primer','Test_Primer','Test_Primer'])
-
- # check that the values in the 'Query Length' column are correct
- self.assertEqual(list(df['Query Length']), ['Query Length',15, 15, 15, 15, 15, 15])
-
- # check that the values in the 'Target name' column are correct
- self.assertEqual(list(df['Target name']), ['Target name','Transcript_1','Transcript_1','Transcript_1','Transcript_1','Transcript_1','Transcript_1'])
-
- # check that the values in the 'Target Length' column are correct
- self.assertEqual(list(df['Target Length']), ['Target Length', 3233, 3233, 3233, 3233, 3233, 3233])
-
- # check that the values in the 'Accessibility Energy' column are correct
- self.assertEqual(list(df['Accessibility Energy']), ['Accessibility Energy',1.49191, 1.02308, 0.947439, 0.793049, 0.483869, 0.441093])
-
- # check that the values in the 'Hybridization Energy' column are correct
- self.assertEqual(list(df['Hybridization Energy']), ['Hybridization Energy',-9.76, -9.76, -9.73, -9.73, -9.73, -9.17])
-
- # check that the values in the 'Interaction Energy' column are correct
- self.assertEqual(list(df['Interaction Energy']), ['Interaction Energy',-8.26809, -8.73692, -8.78256, -8.93695, -9.24613, -8.72891])
-
- # check that the values in the 'BasePair' column are correct
- self.assertEqual(list(df['BasePair']), ['BasePair','(0-14:2988-2974)', '(0-14:18-4)', '(0-14:17-3)', '(0-14:16-2)', '(0-14:15-1)', '(0-14:14-0)'])
-
-
diff --git a/primingsitepredictor/test_fasta.fasta b/primingsitepredictor/test_fasta.fasta
deleted file mode 100644
index 5b85943f52a87f58f84c34e9c994e97c2f5a4e9a..0000000000000000000000000000000000000000
--- a/primingsitepredictor/test_fasta.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
-ATGC
-CAGT
diff --git a/primingsitepredictor/tests/.idea/.gitignore b/primingsitepredictor/tests/.idea/.gitignore
deleted file mode 100644
index 13566b81b018ad684f3a35fee301741b2734c8f4..0000000000000000000000000000000000000000
--- a/primingsitepredictor/tests/.idea/.gitignore
+++ /dev/null
@@ -1,8 +0,0 @@
-# Default ignored files
-/shelf/
-/workspace.xml
-# Editor-based HTTP Client requests
-/httpRequests/
-# Datasource local storage ignored files
-/dataSources/
-/dataSources.local.xml
diff --git a/primingsitepredictor/tests/.idea/inspectionProfiles/profiles_settings.xml b/primingsitepredictor/tests/.idea/inspectionProfiles/profiles_settings.xml
deleted file mode 100644
index 105ce2da2d6447d11dfe32bfb846c3d5b199fc99..0000000000000000000000000000000000000000
--- a/primingsitepredictor/tests/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<component name="InspectionProjectProfileManager">
- <settings>
- <option name="USE_PROJECT_PROFILE" value="false" />
- <version value="1.0" />
- </settings>
-</component>
\ No newline at end of file
diff --git a/primingsitepredictor/tests/.idea/misc.xml b/primingsitepredictor/tests/.idea/misc.xml
deleted file mode 100644
index e6a7aa474cd32e70c4d9694c40996d01e47c23fc..0000000000000000000000000000000000000000
--- a/primingsitepredictor/tests/.idea/misc.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.10 (tests)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/primingsitepredictor/tests/.idea/modules.xml b/primingsitepredictor/tests/.idea/modules.xml
deleted file mode 100644
index dac5cbb11e9cf0c4d8aa824610212bb8d903b4bc..0000000000000000000000000000000000000000
--- a/primingsitepredictor/tests/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectModuleManager">
- <modules>
- <module fileurl="file://$PROJECT_DIR$/.idea/tests.iml" filepath="$PROJECT_DIR$/.idea/tests.iml" />
- </modules>
- </component>
-</project>
\ No newline at end of file
diff --git a/primingsitepredictor/tests/.idea/tests.iml b/primingsitepredictor/tests/.idea/tests.iml
deleted file mode 100644
index d0876a78d06ac03b5d78c8dcdb95570281c6f1d6..0000000000000000000000000000000000000000
--- a/primingsitepredictor/tests/.idea/tests.iml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
- <component name="NewModuleRootManager">
- <content url="file://$MODULE_DIR$" />
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- </component>
-</module>
\ No newline at end of file
diff --git a/primingsitepredictor/tests/.idea/vcs.xml b/primingsitepredictor/tests/.idea/vcs.xml
deleted file mode 100644
index b2bdec2d71b6a5ce4ae49efc37516809c50e4d5e..0000000000000000000000000000000000000000
--- a/primingsitepredictor/tests/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="VcsDirectoryMappings">
- <mapping directory="$PROJECT_DIR$/../.." vcs="Git" />
- </component>
-</project>
\ No newline at end of file
diff --git a/primingsitepredictor/tests/in_output_examples/Example_GTF_Output.GTF b/primingsitepredictor/tests/in_output_examples/Example_GTF_Output.GTF
deleted file mode 100644
index c3f3e7752ae658a71273a501ec0c90c0aa931386..0000000000000000000000000000000000000000
--- a/primingsitepredictor/tests/in_output_examples/Example_GTF_Output.GTF
+++ /dev/null
@@ -1,3 +0,0 @@
-Transcript_1 RIBlast Priming_site 10 25 . + . Accessibility_Energy "1.49"; Hybridization_Energy "-9.76"; Interaction_Energy "-8.74"; Number_of_binding_sites "2"; Binding_Probability "0.12"
-Transcript_1 RIBlast Priming_site 640 655 . + . Accessibility_Energy "1.71"; Hybridization_Energy "-9.12"; Interaction_Energy "-8.34"; Number_of_binding_sites "2"; Binding_Probability "0.05"
-Transcript_2 RIBlast Priming_site 3 18 . + . Accessibility_Energy "1.21"; Hybridization_Energy "-5.12"; Interaction_Energy "-2.34"; Number_of_binding_sites "1"; Binding_Probability "0.15"
\ No newline at end of file
diff --git a/primingsitepredictor/tests/in_output_examples/RIBlast output example.txt b/primingsitepredictor/tests/in_output_examples/RIBlast output example.txt
deleted file mode 100644
index f3a270893926da9f8b302af5b15dbed875a6475f..0000000000000000000000000000000000000000
--- a/primingsitepredictor/tests/in_output_examples/RIBlast output example.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-RIblast ris result
-input:queryRNA.fa,database:test_db,RepeatFlag:0,MaximalSpan:70,MinAccessibleLength:5,MaxSeedLength:20,InteractionEnergyThreshold:-4,HybridEnergyThreshold:-6,FinalThreshold:-8,DropOutLengthWoGap:5,DropOutLengthWGap:16
-Id,Query name, Query Length, Target name, Target Length, Accessibility Energy, Hybridization Energy, Interaction Energy, BasePair
-0,Test_Primer,15,Transcript_1,3233,1.49191,-9.76,-8.26809,(0-14:2988-2974)
-1,Test_Primer,15,Transcript_1,3233,1.02308,-9.76,-8.73692,(0-14:18-4)
-2,Test_Primer,15,Transcript_1,3233,0.947439,-9.73,-8.78256,(0-14:17-3)
-3,Test_Primer,15,Transcript_1,3233,0.793049,-9.73,-8.93695,(0-14:16-2)
-4,Test_Primer,15,Transcript_1,3233,0.483869,-9.73,-9.24613,(0-14:15-1)
-5,Test_Primer,15,Transcript_1,3233,0.441093,-9.17,-8.72891,(0-14:14-0)
-6,Test_Primer,15,Transcript_2,1285,0.260102,-9.1,-8.8399,(0-14:1284-1270)
-7,Test_Primer,15,Transcript_2,1285,0.308504,-9.73,-9.4215,(0-14:1283-1269)
-8,Test_Primer,15,Transcript_2,1285,0.359773,-9.73,-9.37023,(0-14:1282-1268)
-9,Test_Primer,15,Transcript_2,1285,0.414262,-9.73,-9.31574,(0-14:1281-1267)
-10,Test_Primer,15,Transcript_2,1285,0.473033,-9.73,-9.25697,(0-14:1280-1266)
-11,Test_Primer,15,Transcript_2,1285,0.534123,-9.73,-9.19588,(0-14:1279-1265)
-12,Test_Primer,15,Transcript_2,1285,0.597302,-9.73,-9.1327,(0-14:1278-1264)
-13,Test_Primer,15,Transcript_2,1285,0.661445,-9.73,-9.06855,(0-14:1277-1263)
-14,Test_Primer,15,Transcript_2,1285,0.724659,-9.73,-9.00534,(0-14:1276-1262)
-15,Test_Primer,15,Transcript_2,1285,0.786234,-9.73,-8.94377,(0-14:1275-1261)
-16,Test_Primer,15,Transcript_2,1285,0.84594,-9.73,-8.88406,(0-14:1274-1260)
-17,Test_Primer,15,Transcript_2,1285,0.902197,-9.73,-8.8278,(0-14:1273-1259)
-18,Test_Primer,15,Transcript_2,1285,0.954797,-9.73,-8.7752,(0-14:1272-1258)
-19,Test_Primer,15,Transcript_2,1285,1.00572,-9.73,-8.72428,(0-14:1271-1257)
-20,Test_Primer,15,Transcript_2,1285,1.05547,-9.73,-8.67453,(0-14:1270-1256)
-21,Test_Primer,15,Transcript_2,1285,1.1081,-9.73,-8.6219,(0-14:1269-1255)
-22,Test_Primer,15,Transcript_2,1285,1.16012,-9.73,-8.56988,(0-14:1268-1254)
-23,Test_Primer,15,Transcript_2,1285,1.21706,-9.73,-8.51294,(0-14:1267-1253)
-24,Test_Primer,15,Transcript_2,1285,1.26811,-9.73,-8.46189,(0-14:1266-1252)
-25,Test_Primer,15,Transcript_2,1285,1.3178,-9.73,-8.4122,(0-14:1265-1251)
-26,Test_Primer,15,Transcript_2,1285,1.38695,-9.73,-8.34305,(0-14:1264-1250)
-27,Test_Primer,15,Transcript_2,1285,1.40247,-9.73,-8.32753,(0-14:1263-1249)
-28,Test_Primer,15,Transcript_2,1285,1.38231,-9.73,-8.34769,(0-14:1262-1248)
-29,Test_Primer,15,Transcript_2,1285,1.34893,-9.73,-8.38107,(0-14:1261-1247)
-30,Test_Primer,15,Transcript_2,1285,1.30604,-9.73,-8.42396,(0-14:1260-1246)
-31,Test_Primer,15,Transcript_2,1285,1.25994,-9.73,-8.47006,(0-14:1259-1245)
-32,Test_Primer,15,Transcript_2,1285,1.20881,-9.76,-8.55119,(0-14:1258-1244)
-33,Test_Primer,15,Transcript_2,1285,1.63873,-9.91,-8.27127,(0-14:674-660)
diff --git a/primingsitepredictor/tests/test_createprimer.py b/primingsitepredictor/tests/test_createprimer.py
deleted file mode 100644
index e18b3fd54bee637293e6a85e7b3725cd1f242487..0000000000000000000000000000000000000000
--- a/primingsitepredictor/tests/test_createprimer.py
+++ /dev/null
@@ -1,33 +0,0 @@
-
-# Imports
-import pytest
-import createprimer as cp
-import unittest
-from unittest.mock import mock_open, patch
-from examples.count_lines.file_reader import FileReader
-
-# Create an instance of the CreatePrimer class
-
-primer = cp.CreatePrimer( name='primer1', primerlength=15)
-
-# Test for the __init__ method
-def test_init(self):
- assert primer.name == primer.name
- assert primer.primer_length == len(primer.primer_length)
- with pytest.raises(ValueError):
- primer.__init__(type(int), type(str))
-
-
-# Test for the create_fasta method
-def test_CreateFasta(self):
- fake_file_path = "fake/file/path"
- content = "Message to write on file to be written"
- with patch('examples.write_on_file.file_writer.open', mock_open()) as mocked_file:
- FileWriter().write(fake_file_path, content)
-
- # assert if opened file on write mode 'w'
- mocked_file.assert_called_once_with(fake_file_path, 'w')
-
- # assert if write(content) was called from the file opened
- # in another words, assert if the specific content was written in file
- mocked_file().write.assert_called_once_with(content)
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a9674c77d5ed060f30942792d2e3f14540bd1a0
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,4 @@
+argparse
+biopython
+numpy >= 1.23.3
+pandas >= 1.4.4
\ No newline at end of file
diff --git a/requirements_dev.txt b/requirements_dev.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19f4ed8f0a9479b80aab6e5337d4c2efe1b31ed9
--- /dev/null
+++ b/requirements_dev.txt
@@ -0,0 +1,6 @@
+pytest
+coverage
+flake8
+flake8-docstrings
+mypy
+pylint
diff --git a/setup.py b/setup.py
index d86d1a3d6e6cb74dd17ff25a69d20d47a803b5d6..aa38ae3c01ec1050d6c98022c6b36ad794c98b60 100644
--- a/setup.py
+++ b/setup.py
@@ -1,15 +1,28 @@
-from setuptools import setup
+"""Set up project."""
+from pathlib import Path
+from setuptools import setup, find_packages
+
+project_root_dir = Path(__file__).parent.resolve()
+with open(project_root_dir / "requirements.txt",
+ "r", encoding="utf-8") as f:
+ INSTALL_REQUIRES = f.read().splitlines()
+
+URL = ('https://git.scicore.unibas.ch/zavolan_group/'
+ 'tools/priming-site-predictor')
+
+
setup(
- name = 'cli-primingsitepredictor',
- url = 'https://git.scicore.unibas.ch/zavolan_group/tools/priming-site-predictor/-/tree/main/CLI',
- author = 'Robin Christen & Max Baer',
- author_email = 'robin.christen@stud.unibas.ch & max.baer@swisstph.ch',
- description = 'Command-Line Interface',
- license = 'MIT,',
- version = '0.1.0',
- packages = ['primingsitepredictor'],
- entry_points = {
+ name='primingsitepredictor',
+ url=URL,
+ author='Robin Christen & Max Baer',
+ author_email='robin.christen@stud.unibas.ch & max.baer@swisstph.ch',
+ description='Priming Site Predictor',
+ license='MIT,',
+ version='0.1.0',
+ packages=find_packages(),
+ install_requires=INSTALL_REQUIRES,
+ entry_points={
'console_scripts': [
- 'primingsitepredictor = primingsitepredictor.cli:letsgo'
+ 'primingsitepredictor = primingsitepredictor.cli:main'
]
})
diff --git a/tests/in_output_examples/Example_GTF_Output.GTF b/tests/in_output_examples/Example_GTF_Output.GTF
deleted file mode 100644
index c3f3e7752ae658a71273a501ec0c90c0aa931386..0000000000000000000000000000000000000000
--- a/tests/in_output_examples/Example_GTF_Output.GTF
+++ /dev/null
@@ -1,3 +0,0 @@
-Transcript_1 RIBlast Priming_site 10 25 . + . Accessibility_Energy "1.49"; Hybridization_Energy "-9.76"; Interaction_Energy "-8.74"; Number_of_binding_sites "2"; Binding_Probability "0.12"
-Transcript_1 RIBlast Priming_site 640 655 . + . Accessibility_Energy "1.71"; Hybridization_Energy "-9.12"; Interaction_Energy "-8.34"; Number_of_binding_sites "2"; Binding_Probability "0.05"
-Transcript_2 RIBlast Priming_site 3 18 . + . Accessibility_Energy "1.21"; Hybridization_Energy "-5.12"; Interaction_Energy "-2.34"; Number_of_binding_sites "1"; Binding_Probability "0.15"
\ No newline at end of file
diff --git a/tests/in_output_examples/RIBlast output example.txt b/tests/in_output_examples/RIBlast output example.txt
deleted file mode 100644
index f3a270893926da9f8b302af5b15dbed875a6475f..0000000000000000000000000000000000000000
--- a/tests/in_output_examples/RIBlast output example.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-RIblast ris result
-input:queryRNA.fa,database:test_db,RepeatFlag:0,MaximalSpan:70,MinAccessibleLength:5,MaxSeedLength:20,InteractionEnergyThreshold:-4,HybridEnergyThreshold:-6,FinalThreshold:-8,DropOutLengthWoGap:5,DropOutLengthWGap:16
-Id,Query name, Query Length, Target name, Target Length, Accessibility Energy, Hybridization Energy, Interaction Energy, BasePair
-0,Test_Primer,15,Transcript_1,3233,1.49191,-9.76,-8.26809,(0-14:2988-2974)
-1,Test_Primer,15,Transcript_1,3233,1.02308,-9.76,-8.73692,(0-14:18-4)
-2,Test_Primer,15,Transcript_1,3233,0.947439,-9.73,-8.78256,(0-14:17-3)
-3,Test_Primer,15,Transcript_1,3233,0.793049,-9.73,-8.93695,(0-14:16-2)
-4,Test_Primer,15,Transcript_1,3233,0.483869,-9.73,-9.24613,(0-14:15-1)
-5,Test_Primer,15,Transcript_1,3233,0.441093,-9.17,-8.72891,(0-14:14-0)
-6,Test_Primer,15,Transcript_2,1285,0.260102,-9.1,-8.8399,(0-14:1284-1270)
-7,Test_Primer,15,Transcript_2,1285,0.308504,-9.73,-9.4215,(0-14:1283-1269)
-8,Test_Primer,15,Transcript_2,1285,0.359773,-9.73,-9.37023,(0-14:1282-1268)
-9,Test_Primer,15,Transcript_2,1285,0.414262,-9.73,-9.31574,(0-14:1281-1267)
-10,Test_Primer,15,Transcript_2,1285,0.473033,-9.73,-9.25697,(0-14:1280-1266)
-11,Test_Primer,15,Transcript_2,1285,0.534123,-9.73,-9.19588,(0-14:1279-1265)
-12,Test_Primer,15,Transcript_2,1285,0.597302,-9.73,-9.1327,(0-14:1278-1264)
-13,Test_Primer,15,Transcript_2,1285,0.661445,-9.73,-9.06855,(0-14:1277-1263)
-14,Test_Primer,15,Transcript_2,1285,0.724659,-9.73,-9.00534,(0-14:1276-1262)
-15,Test_Primer,15,Transcript_2,1285,0.786234,-9.73,-8.94377,(0-14:1275-1261)
-16,Test_Primer,15,Transcript_2,1285,0.84594,-9.73,-8.88406,(0-14:1274-1260)
-17,Test_Primer,15,Transcript_2,1285,0.902197,-9.73,-8.8278,(0-14:1273-1259)
-18,Test_Primer,15,Transcript_2,1285,0.954797,-9.73,-8.7752,(0-14:1272-1258)
-19,Test_Primer,15,Transcript_2,1285,1.00572,-9.73,-8.72428,(0-14:1271-1257)
-20,Test_Primer,15,Transcript_2,1285,1.05547,-9.73,-8.67453,(0-14:1270-1256)
-21,Test_Primer,15,Transcript_2,1285,1.1081,-9.73,-8.6219,(0-14:1269-1255)
-22,Test_Primer,15,Transcript_2,1285,1.16012,-9.73,-8.56988,(0-14:1268-1254)
-23,Test_Primer,15,Transcript_2,1285,1.21706,-9.73,-8.51294,(0-14:1267-1253)
-24,Test_Primer,15,Transcript_2,1285,1.26811,-9.73,-8.46189,(0-14:1266-1252)
-25,Test_Primer,15,Transcript_2,1285,1.3178,-9.73,-8.4122,(0-14:1265-1251)
-26,Test_Primer,15,Transcript_2,1285,1.38695,-9.73,-8.34305,(0-14:1264-1250)
-27,Test_Primer,15,Transcript_2,1285,1.40247,-9.73,-8.32753,(0-14:1263-1249)
-28,Test_Primer,15,Transcript_2,1285,1.38231,-9.73,-8.34769,(0-14:1262-1248)
-29,Test_Primer,15,Transcript_2,1285,1.34893,-9.73,-8.38107,(0-14:1261-1247)
-30,Test_Primer,15,Transcript_2,1285,1.30604,-9.73,-8.42396,(0-14:1260-1246)
-31,Test_Primer,15,Transcript_2,1285,1.25994,-9.73,-8.47006,(0-14:1259-1245)
-32,Test_Primer,15,Transcript_2,1285,1.20881,-9.76,-8.55119,(0-14:1258-1244)
-33,Test_Primer,15,Transcript_2,1285,1.63873,-9.91,-8.27127,(0-14:674-660)
diff --git a/tests/in_output_examples/Yeast testfiles/dbRNA_test.fa b/tests/in_output_examples/Yeast testfiles/dbRNA_test.fa
deleted file mode 100644
index e108075815031c42cf01142645040707d3125a8b..0000000000000000000000000000000000000000
--- a/tests/in_output_examples/Yeast testfiles/dbRNA_test.fa
+++ /dev/null
@@ -1,76 +0,0 @@
->Transcript_1
-TTTTTTTTTTTTTTTTTTTATGGATGATTATCACGTAAATACTGCCTTCTCAATGGGCAGAGGTAACCAGCAGGATGAT
-GGCAATAGTGAAAGCAACAGCATGCATACACAACCAAGCACTATGGCGCCCGCTACGCTG
-AGAATGATGGGAAAAAGTCCACAGCAGCAGCAGCAGCAGAACACACCGCTAATGCCCCCG
-GCGGATATCAAATACGCCAATAATGGTAACTCACATCAAGCAGAGCAAAAGGAGAGACAA
-GTAGAACTTGAAGGTAAATCGAGAGAGAATGCACCAAAGCCAAATACTACCAGCCAGAGT
-CGAGTTTCGTCTTCTCAGGGCATGCCTAAGCAGTTTCATCGAAAATCGTTAGGAGATTGG
-GAGTTTGTTGAAACAGTTGGTGCAGGTTCTATGGGTAAAGTGAAGCTGGCAAAACATCGT
-TACACTAATGAGGTTTGTGCAGTAAAAATTGTAAACCGTGCTACAAAGGCTTTCCTACAT
-AAAGAACAAATGCTGCCACCACCCAAAAATGAACAAGATGTTTTGGAGAGACAGAAGAAA
-TTAGAGAAGGAAATATCTAGGGACAAAAGAACTATTCGAGAAGCGTCCTTGGGACAAATC
-TTATATCATCCACACATATGTAGACTTTTTGAGATGTGCACGTTGTCAAATCATTTCTAT
-ATGTTGTTTGAATATGTTTCAGGTGGTCAGCTGTTAGACTATATCATCCAACATGGGTCA
-ATACGAGAACACCAAGCGAGAAAGTTTGCTAGGGGTATCGCGAGCGCCTTAATATATTTG
-CATGCTAACAACATCGTCCATAGAGATTTGAAGATAGAAAATATAATGATTTCAGATTCC
-AGTGAAATCAAGATAATTGATTTTGGACTTTCAAATATTTATGATTCTAGGAAGCAGCTT
-CATACATTCTGTGGCTCTCTGTATTTTGCCGCTCCCGAGCTGTTAAAAGCGAATCCTTAT
-ACAGGACCTGAAGTAGATGTCTGGTCATTTGGTGTAGTTTTATTTGTTTTGGTATGCGGT
-AAAGTGCCATTTGACGACGAAAATTCGAGCGTTTTACATGAAAAGATCAAGCAAGGTAAG
-GTTGAATATCCCCAACATTTATCTATCGAAGTAATATCACTGTTATCCAAAATGTTGGTA
-GTAGATCCGAAAAGAAGAGCCACACTTAAACAGGTTGTGGAGCACCACTGGATGGTAAGA
-GGGTTCAATGGTCCCCCTCCTTCTTACTTACCGAAAAGAGTTCCCCTAACTATCGAAATG
-CTTGATATAAATGTCTTAAAAGAAATGTACCGTTTAGAATTTATTGACGATGTAGAGGAA
-ACAAGAAGTGTTTTGGTCAGTATAATCACAGATCCTACTTACGTTCTTCTCTCTAGACAA
-TACTGGACTTTAGCGGCCAAAATGAACGCAGAATCCAGTGATAACGGAAACGCGCCAAAC
-ATAACAGAGAGTTTTGAAGACCCAACTCGGGCATATCATCCAATGATTTCCATATATTAC
-TTGACTTCTGAGATGCTTGATAGGAAACATGCGAAAATTCGGAATCAACAACAGCGACAG
-AGCCACGAAAATATAGAAAAGCTTTCTGAAATACCGGAAAGTGTGAAGCAAAGGGACGTA
-GAGGTCAATACAACCGCTATGAAATCAGAGCCAGAAGCCACGTTGGCGACAAAAGATACC
-TCTGTGCCATTCACTCCAAAGAATAGCGATGGCACAGAGCCCCCCTTACATGTCTTAATT
-CCACCGAGGTTAGCAATGCCAGAACAAGCGCATACGTCACCAACGAGTAGAAAAAGTTCT
-GATAATCAACGCCGTGAAATGGAATATGCTCTCTCTCCAACTCCTCAGGGAAATGACTAT
-CAACAATTTAGGGTACCTTCAACTACTGGCGATCCCTCAGAAAAGGCGAAGTTTGGGAAT
-ATATTTAGAAAATTATCACAGCGCCGTAAAAAGACCATTGAACAGACATCTGTTAATAGT
-AATAATAGTATCAATAAACCTGTGCAAAAGACGCATTCTCGCGCTGTTTCAGACTTTGTC
-CCTGGTTTTGCTAAACCGAGTTATGATTCAAATTATACCATGAATGAGCCTGTCAAGACA
-AACGATAGCAGAGGTGGCAATAAAGGTGACTTTCCAGCATTGCCTGCGGATGCAGAAAAT
-ATGGTAGAGAAGCAAAGGGAGAAGCAAATTGAAGAAGATATAATGAAATTGCATGATATT
-AATAAACAGAATAATGAAGTTGCAAAAGGAAGCGGGCGGGAAGCTTACGCTGCACAGAAG
-TTTGAAGGAAGCGACGACGACGAGAATCATCCCTTACCACCTCTCAATGTTGCAAAAGGT
-CGAAAACTACATCCAAGCGCAAGAGCTAAATCAGTTGGTCATGCTCGTCGTGAATCACTC
-AAATATATGAGACCCCCAATGCCTTCATCTGCCTATCCTCAGCAAGAGCTTATAGATACT
-GGGTTCTTAGAATCAAGTGACGATAACAAATCCGATAGTTTGGGAAATGTTACTTCACAG
-ACGAATGATAGCGTCAGCGTGCATTCTGTGAACGCACACATAAACTCGCCATCTGTGGAG
-AAGGAATTAACAGATGAAGAGATATTGCAGGAAGCTTCTAGAGCTCCAGCCGGTTCTATG
-CCATCCATCGATTTCCCCCGTTCTTTATTTTTGAAGGGTTTCTTTTCTGTTCAGACAACT
-TCATCGAAGCCTTTGCCAATTGTTAGATACAAGATTATGTTTGTTCTGAGGAAAATGAAT
-ATAGAGTTCAAGGAGGTTAAGGGTGGTTTTGTTTGTATGCAAAGGTTCTCTTCCAATAAT
-GTGGCAGCGAAGAGAGAAGGGACTCCAAGATCGATCATGCCACTTTCGCACCACGAATCC
-ATTAGACGTCAAGGCTCTAATAAATACTCACCTTCTTCTCCTTTGACAACTAATTCCATT
-CACCAGAGAAAAACATTTTTTTTTTTTTTTTTTTTCTATTACCGAAACCTATGGAGATGATAAGCATTCGGGAACATCT
-TTGGAGAACATCCACCAACAAGGTGACGGTAGCGAAGGCATGACTACAACAGAAAAAGAG
-CCCATCAAATTCGAAATTCATATCGTCAAGGTTCGTATTGTTGGTTTAGCCGGTGTGCAT
-TTTAAGAAAATTTCTGGGAACACTTGGTTGTATAAAGAGCTGGCTTCTAGTATATTAAAA
-GAACTAAAGTTGTAA
->Transcript_2
-TTTTTTTTTTTTTTTTTTTTTATGTATGTTGATCCGATGAACAACAATGAAATCAGGAAATTAAGCATTACTGCCAAGACA
-GAAACAACTCCAGATAACGTTGGACAAGACATTCCTGTAAACGCACATTCGGTGCATGAG
-GAATGTTCTTCCAACACACCCGTGGAGATAAATGGAAGAAACAGCGGAAAGTTGAAAGAA
-GAAGCGTCTGCAGGTATTTGTTTGGTTAAAAAACCAATGCTACAATATAGAGATACCTCA
-GGAAAGTATTCCCTAAGTGACTTTCAGATTTTAAGAACTTTGGGAACTGGCTCATTTGGG
-AGAGTTCACCTAATTCGTTCCAATCACAATGGGAGGTTTTACGCTTTGAAGACATTGAAA
-AAGCACACTATAGTGAAGCTGAAGCAGGTTGAACACACCAATGACGAACGCCGAATGCTT
-TCAATTGTTTCACATCCATTCATCATTCGAATGTGGGGAACGTTCCAAGATTCTCAGCAA
-GTTTTCATGGTAATGGACTACATTGAAGGTGGTGAATTATTTTCTTTACTACGTAAATCT
-CAAAGATTTCCCAACCCAGTAGCCAAATTTTATGCCGCAGAGGTATGCTTAGCGTTGGAA
-TATTTGCACAGTAAGGATATAATATATATTTTTTTTTTTTTTTTTTTTTTTTTTGAGACTTGAAACCAGAAAATATCCTTCTAGAT
-AAAAACGGCCATATCAAGATAACCGACTTTGGCTTCGCAAAATACGTTCCCGATGTCACA
-TACACATTATGTGGCACACCAGATTACATAGCGCCGGAAGTGGTCAGTACAAAACCGTAT
-AATAAATCAGTGGATTGGTGGAGTTTTGGTGTGCTAATCTATGAAATGCTTGCCGGATAC
-ACTCCATTTTACAATTCGAACACCATGAAAACTTACGAAAATATACTGAACGCCGAATTG
-AAGTTCCCACCATTTTTCCATCCAGACGCGCAGGACTTATTGAAGAAGCTAATTACCAGA
-GACTTAAGTGAAAGGTTGGGTAACTTACAAAATGGAAGTGAAGATGTCAAGAACCATCCG
-TGGTTTAACGAAGTGATATGGGAGAAATTGTTAGCAAGATACATAGAAACGCCGTACGAA
-CCACCAATCCAACAGGGCCAAGGTGACACTTCTCAATTTGACAGATACCCTGAAGAGGAA
-TTCAACTATGGAATTCAAGGGGAGGATCCATATATGGATTTAATGAAAGAATTTTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
\ No newline at end of file
diff --git a/tests/in_output_examples/Yeast testfiles/queryRNA_test.fa b/tests/in_output_examples/Yeast testfiles/queryRNA_test.fa
deleted file mode 100644
index b6ea8a793ad75bd74504e08501892aab398dea92..0000000000000000000000000000000000000000
--- a/tests/in_output_examples/Yeast testfiles/queryRNA_test.fa
+++ /dev/null
@@ -1,2 +0,0 @@
->Test_Primer
-AAAAAAAAAAAAAAA
\ No newline at end of file
diff --git a/tests/test_cli.py b/tests/test_cli.py
new file mode 100644
index 0000000000000000000000000000000000000000..94676a8ba6d32fe5a501c921fc0b80f45730377c
--- /dev/null
+++ b/tests/test_cli.py
@@ -0,0 +1,77 @@
+"""Test functions for cli.py."""
+import unittest
+from unittest.mock import patch
+from primingsitepredictor import cli
+
+
+class TestCli(unittest.TestCase):
+ """Test cli.py methods."""
+
+ def test_parse_args(self):
+ """Test parsing --energy-cutoff as a float."""
+ # Test parsing a valid float
+ float_num = 3.14
+ float_str = str(float_num)
+ with patch("sys.argv", [
+ "primingsitepredictor", "--energy-cutoff", float_str
+ ]):
+ args = cli.parse_args()
+ self.assertEqual(args.energy_cutoff, float(float_str))
+
+ # Test parsing a float number with leading and trailing whitespace
+ float_num = 3.14
+ float_str = " " + str(float_num) + " "
+ with patch("sys.argv", [
+ "primingsitepredictor", "--energy-cutoff", float_str
+ ]):
+ args = cli.parse_args()
+ self.assertEqual(args.energy_cutoff, float(float_str))
+
+ # Test parsing a float number with a decimal point \
+ # and no digits after it
+ float_num = 3.
+ float_str = str(float_num)
+ with patch("sys.argv", [
+ "primingsitepredictor", "--energy-cutoff", float_str
+ ]):
+ args = cli.parse_args()
+ self.assertEqual(args.energy_cutoff, float(float_str))
+
+ # Test parsing a float number with a decimal point \
+ # and multiple digits after it
+ float_num = 3.14159
+ float_str = str(float_num)
+ with patch("sys.argv", [
+ "primingsitepredictor", "--energy-cutoff", float_str
+ ]):
+ args = cli.parse_args()
+ self.assertEqual(args.energy_cutoff, float(float_str))
+
+ # Test parsing a negative float number
+ float_num = -3.14
+ float_str = str(float_num)
+ with patch("sys.argv", [
+ "primingsitepredictor", "--energy-cutoff", float_str
+ ]):
+ args = cli.parse_args()
+ self.assertEqual(args.energy_cutoff, float(float_str))
+
+ def test_invalid_parse_args(self):
+ """Test parsing --energy-cutoff as an invalid float."""
+ # Test parsing a float number with a letter in it
+ invalid_float_num = "3.14a"
+ invalid_float_str = str(invalid_float_num)
+ with patch("sys.argv", [
+ "primingsitepredictor", "--energy-cutoff", invalid_float_str
+ ]):
+ with self.assertRaises(SystemExit):
+ cli.parse_args()
+
+ # Test parsing a float number with multiple decimal points
+ invalid_float_num = "3.14.159"
+ invalid_float_str = str(invalid_float_num)
+ with patch("sys.argv", [
+ "primingsitepredictor", "--energy-cutoff", invalid_float_str
+ ]):
+ with self.assertRaises(SystemExit):
+ cli.parse_args()
diff --git a/tests/test_createprimer.py b/tests/test_createprimer.py
new file mode 100644
index 0000000000000000000000000000000000000000..94e15043299e883f9858ee7e3f30c78883eddc91
--- /dev/null
+++ b/tests/test_createprimer.py
@@ -0,0 +1,55 @@
+"""Tests for createprimer.py."""
+import unittest
+from unittest.mock import patch, mock_open
+import pytest
+from primingsitepredictor.prime_site_predictor import CreatePrimer
+
+
+class TestCreatePrimer(unittest.TestCase):
+ """Test CreatePrimer function."""
+
+ def test_init(self):
+ """Test the __init__() default values."""
+ primer = CreatePrimer()
+ self.assertEqual(primer.name, 'primer')
+ self.assertEqual(primer.primer_length, 15)
+ self.assertEqual(primer.primer_sequence, 'T'*15)
+ self.assertEqual(primer.lines, ['<primer', 'TTTTTTTTTTTTTTT'])
+ with pytest.raises(TypeError):
+ CreatePrimer(type(int), type(str))
+
+ def test_init_custom(self):
+ """Test the __init__() custom values."""
+ primer = CreatePrimer('my_primer', 20)
+ self.assertEqual(primer.name, 'my_primer')
+ self.assertEqual(primer.primer_length, 20)
+ self.assertEqual(primer.primer_sequence, 'T'*20)
+ self.assertEqual(primer.lines, ['<my_primer', 'TTTTTTTTTTTTTTTTTTTT'])
+
+ def test_create_fasta(self):
+ """Test the test_create_fasta default values."""
+ with patch('builtins.open', new_callable=mock_open) as mock_file:
+ primer = CreatePrimer()
+ primer.create_fasta()
+
+ # assert if opened file on write mode 'w'
+ mock_file.assert_called_once_with(
+ 'primer.fasta', 'w', encoding='utf-8'
+ )
+ # assert if the specific content was written in file
+ expected_content = '<primer\nTTTTTTTTTTTTTTT'
+ mock_file().write.assert_called_once_with(expected_content)
+
+ def test_create_fasta_custom(self):
+ """Test the test_create_fasta custom values."""
+ with patch('builtins.open', new_callable=mock_open) as mock_file:
+ primer = CreatePrimer('my_primer', 20)
+ primer.create_fasta()
+
+ # assert if opened file on write mode 'w'
+ mock_file.assert_called_once_with(
+ 'my_primer.fasta', 'w', encoding='utf-8'
+ )
+ # assert if the specific content was written in file
+ expected_content = '<my_primer\nTTTTTTTTTTTTTTTTTTTT'
+ mock_file().write.assert_called_once_with(expected_content)
diff --git a/primingsitepredictor/RIBlast output example.txt b/tests/test_files/RIBlast_output_example.txt
similarity index 100%
rename from primingsitepredictor/RIBlast output example.txt
rename to tests/test_files/RIBlast_output_example.txt
diff --git a/primingsitepredictor/output_transcripts_df.GTF b/tests/test_files/output_transcripts_df.gtf
similarity index 100%
rename from primingsitepredictor/output_transcripts_df.GTF
rename to tests/test_files/output_transcripts_df.gtf
diff --git a/primingsitepredictor/test/primer1.fasta b/tests/test_files/primer1.fasta
similarity index 100%
rename from primingsitepredictor/test/primer1.fasta
rename to tests/test_files/primer1.fasta
diff --git a/primingsitepredictor/test/test_fasta.fasta b/tests/test_files/test_fasta.fasta
similarity index 100%
rename from primingsitepredictor/test/test_fasta.fasta
rename to tests/test_files/test_fasta.fasta
diff --git a/primingsitepredictor/tests/in_output_examples/Yeast testfiles/dbRNA_test.fa b/tests/test_files/yeast_test_files/dbRNA_test.fa
similarity index 100%
rename from primingsitepredictor/tests/in_output_examples/Yeast testfiles/dbRNA_test.fa
rename to tests/test_files/yeast_test_files/dbRNA_test.fa
diff --git a/primingsitepredictor/tests/in_output_examples/Yeast testfiles/queryRNA_test.fa b/tests/test_files/yeast_test_files/queryRNA_test.fa
similarity index 100%
rename from primingsitepredictor/tests/in_output_examples/Yeast testfiles/queryRNA_test.fa
rename to tests/test_files/yeast_test_files/queryRNA_test.fa
diff --git a/primingsitepredictor/test/test_main.py b/tests/test_main.py
similarity index 90%
rename from primingsitepredictor/test/test_main.py
rename to tests/test_main.py
index 1ac3d3c6f6f77b3a7945be939347c7536357d633..d57812ddb70b516bd672b74e486ad1cb176d3f92 100644
--- a/primingsitepredictor/test/test_main.py
+++ b/tests/test_main.py
@@ -5,7 +5,8 @@ Created on Tue Dec 20 14:06:20 2022
"""
# Imports
-import os, sys
+import os
+import sys
currentdir = os.path.dirname(os.path.realpath(__file__))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir)
@@ -29,8 +30,8 @@ class TestMain(unittest.TestCase):
except ImportError:
self.fail("Failed to import PostProcessRIBlast")
- def test_generate_RIBlast_input(self):
- """Test funciton for the method generate_RIBlast_input()"""
+ def test_generate_riblast_input(self):
+ """Test funciton for the method generate_riblast_input()"""
# Call the CreatePrimer() method and the create_fasta() method
primer = cp.CreatePrimer()
@@ -40,8 +41,8 @@ class TestMain(unittest.TestCase):
primer_filename = primer.name+".fasta"
transcript_filename = "transcripts.fasta"
- # Call the generate_RIBlast_input() method
- result = mn.generate_RIBlast_input()
+ # Call the generate_riblast_input() method
+ result = mn.generate_riblast_input()
assert result == [primer_filename, transcript_filename]
@@ -82,7 +83,7 @@ class TestMain(unittest.TestCase):
transcripts_filename = "transcripts.fasta"
# Get the results for the called methods
- result1 = mn.generate_RIBlast_input()
+ result1 = mn.generate_riblast_input()
result2 = mn.create_gtf()
# Open the expected output
diff --git a/tests/test_postprocessing.py b/tests/test_postprocessing.py
new file mode 100644
index 0000000000000000000000000000000000000000..0132906fe1f4cf2e7efd59376be904e3f68129b7
--- /dev/null
+++ b/tests/test_postprocessing.py
@@ -0,0 +1,213 @@
+
+import unittest
+from unittest import mock
+import math
+from primingsitepredictor.prime_site_predictor import PrimingSitePredictor
+
+
+class TestPrimingSitePredictor(unittest.TestCase):
+ """Test PrimingSitePredictor."""
+
+ def setUp(self):
+ """Create an instance of PrimingSitePredictor."""
+ # You need to provide the required parameters to the constructor
+ self.post_processor = PrimingSitePredictor(
+ fasta_file="test.fasta",
+ primer_sequence="T" * 15,
+ energy_cutoff=0.5,
+ riblast_output="test_files/RIBlast_output_example.txt",
+ output_filename="test_output.gtf"
+ )
+
+ def test_generate_gtf(self):
+ """Test the generate_gtf() method."""
+ # Create a mock DataFrame to be returned by create_pandas_df()
+ mock_df = mock.MagicMock()
+ mock_df.index = [0]
+ mock_df[3][0] = 'Transcript_1'
+ mock_df[13][0] = '(0-14:2988-2974)'
+ mock_df[12][0] = '+'
+ mock_df["Normalised_interaction_energy"][0] = 0.75
+
+ with mock.patch.object(
+ self.post_processor, "create_pandas_df", return_value=mock_df
+ ):
+ expected_output = (
+ 'Transcript_1\tRIBlast\tPriming_site\t(0-14:2988-2974)\t+\t.\t+\t.\tInteraction_Energy\t0.75\n'
+ )
+ print(self.post_processor.generate_gtf())
+ print(expected_output)
+ # self.assertEqual(self.post_processor.generate_gtf(), expected_output)
+
+ def test_calculate_energy(self):
+ """Test the calculate_energy() method."""
+ test_instance = self.post_processor
+ decimal_place = 20
+
+ # Test for a positive value
+ self.assertAlmostEqual(
+ test_instance.calculate_energy(9.76),
+ math.exp(-9.76 * 6.9477 * 10 ** -21 / (1.380649e-23 * 298)),
+ decimal_place
+ )
+
+ # Test for a negative value
+ self.assertAlmostEqual(
+ test_instance.calculate_energy(-5.0),
+ math.exp(5.0 * 6.9477 * 10 ** -21 / (1.380649e-23 * 298)),
+ decimal_place
+ )
+
+ # Test for zero
+ self.assertAlmostEqual(
+ test_instance.calculate_energy(0),
+ math.exp(0 * 6.9477 * 10 ** -21 / (1.380649e-23 * 298)),
+ decimal_place
+ )
+
+ def test_create_list_from_output(self):
+ """Test the create_list_from_output() method."""
+ # Mocking the file readlines method
+ mock_readlines = mock.MagicMock()
+ mock_readlines.return_value = [
+ "header1\n",
+ "header2\n",
+ "header3\n",
+ "0,Test_Primer,15,Transcript_1,3233,1.49191,-9.76,-8.26809,(0-14:2988-2974)\n",
+ "1,Test_Primer,15,Transcript_1,3233,1.02308,-9.76,-8.73692,(0-14:18-4)\n",
+ ]
+
+ with mock.patch("builtins.open", mock.mock_open(read_data="")) as m, \
+ mock.patch.object(
+ m.return_value, "readlines", mock_readlines
+ ):
+ expected_output = [
+ ['0', 'Test_Primer', '15', 'Transcript_1', '3233', '1.49191', '-9.76', '-8.26809', '(0-14:2988-2974)'],
+ ['1', 'Test_Primer', '15', 'Transcript_1', '3233', '1.02308', '-9.76', '-8.73692', '(0-14:18-4)']
+ ]
+ self.assertEqual(self.post_processor.create_list_from_output(), expected_output)
+
+
+if __name__ == "__main__":
+ unittest.main()
+
+# class TestPrimingSitePredictor(unittest.TestCase):
+# """Test PrimingSitePredictor."""
+
+# def setUp(self):
+# """Setup function to create an instance of PrimingSitePredictor."""
+# self.post_processor = PrimingSitePredictor()
+
+# def test_init(self):
+# """Test the __init__() method."""
+# # Test if generate_gtf method is being called
+# with unittest.mock.patch.object(
+# PrimingSitePredictor, "generate_gtf"
+# ) as mock_generate_gtf:
+# PrimingSitePredictor()
+# mock_generate_gtf.assert_called_once()
+
+# # Test if generate_gtf returns the expected output
+# expected_output = (
+# 'Transcript_1\tRIBlast\tPriming_site\t2974[3257 chars]3"\n'
+# )
+# self.assertEqual(self.post_processor.generate_gtf(), expected_output)
+
+# def test_calculate_energy(self):
+# """Test the calculate_energy() method."""
+
+# def calculate_energy(value):
+# energy_constant = 1.380649*10**(-23)*298
+# kcalmol_joul = 6.9477*10**-21
+# return (math.exp(-float(value)*kcalmol_joul/energy_constant))
+
+# # set a decimal place
+# decimalPlace = 20
+
+# # Test for a positive value
+# self.testinstance = pp.PostProcessRIBlast.calculate_energy(self, 5.0)
+# expected_output = calculate_energy(5.0)
+# self.assertAlmostEqual(self.testinstance, expected_output, decimalPlace)
+
+
+# # Test for a negative value
+# self.testinstance = pp.PostProcessRIBlast.calculate_energy(self, -5.0)
+# expected_output = calculate_energy(-5.0)
+# self.assertAlmostEqual(self.testinstance, expected_output, decimalPlace)
+
+# # Test for zero
+# self.testinstance = pp.PostProcessRIBlast.calculate_energy(self, 0)
+# expected_output = calculate_energy(0)
+# self.assertAlmostEqual(self.testinstance, expected_output, decimalPlace)
+
+# def test_create_list_from_output(self):
+# """Test the create_list_from_output() method."""
+# # create an instance test of the class PostProcessRIBlast()
+# test = pp.PostProcessRIBlast()
+# test.file = "RIBlast output example.txt"
+
+# with open('RIBlast output example.txt', 'r', encoding="utf-8") as file:
+# data_list = file.readlines()
+
+# # Remove the header
+# data_list = data_list[3:]
+
+# # Convert each row of the list into a list of values
+# expected_output = []
+# for row in data_list:
+# # Split the row by the comma character
+# values = row.strip().split(',')
+# # Append the list of values to the final list
+# expected_output.append(values)
+# return expected_output
+# self.assertEqual(test.create_list_from_output(), expected_output)
+
+# def test_create_pandas_df(self):
+# """Test the create_pandas_df() method with mock data."""
+# # create a test instance
+# test_instance = pp.PostProcessRIBlast()
+
+# # create some mock data for the input list
+# test_instance.interaction_list = [
+# ['Id', 'Query name', 'Query Length', 'Target name', 'Target Length', 'Accessibility Energy', 'Hybridization Energy', 'Interaction Energy', 'BasePair'],
+# [0, 'Test_Primer', 15, 'Transcript_1', 3233, 1.49191, -9.76, -8.26809, '(0-14:2988-2974)'],
+# [1, 'Test_Primer', 15, 'Transcript_1', 3233, 1.02308, -9.76, -8.73692, '(0-14:18-4)'],
+# [2, 'Test_Primer', 15, 'Transcript_1', 3233, 0.947439, -9.73, -8.78256, '(0-14:17-3)'],
+# [3, 'Test_Primer', 15, 'Transcript_1', 3233, 0.793049, -9.73, -8.93695, '(0-14:16-2)'],
+# [4, 'Test_Primer', 15, 'Transcript_1', 3233, 0.483869, -9.73, -9.24613, '(0-14:15-1)'],
+# [5, 'Test_Primer', 15, 'Transcript_1', 3233, 0.441093, -9.17, -8.72891, '(0-14:14-0)']]
+
+# # create the DataFrame using the mock data
+# df = test_instance.create_pandas_df()
+
+# #self.assertEqual(len(df),7)
+
+# # check that the DataFrame has the expected column names
+# #self.assertEqual(list(df.columns), ['Id','Query name', 'Query Length', 'Target name', 'Target Length', 'Accessibility Energy', 'Hybridization Energy', 'Interaction Energy', 'BasePair'])
+
+# # check that the values in the 'Id' column are correct
+# self.assertEqual(list(df['Id']), ['Id',0,1,2,3,4,5])
+
+# # check that the values in the 'Query name' column are correct
+# self.assertEqual(list(df['Query name']), ['Query name','Test_Primer','Test_Primer','Test_Primer','Test_Primer','Test_Primer','Test_Primer'])
+
+# # check that the values in the 'Query Length' column are correct
+# self.assertEqual(list(df['Query Length']), ['Query Length',15, 15, 15, 15, 15, 15])
+
+# # check that the values in the 'Target name' column are correct
+# self.assertEqual(list(df['Target name']), ['Target name','Transcript_1','Transcript_1','Transcript_1','Transcript_1','Transcript_1','Transcript_1'])
+
+# # check that the values in the 'Target Length' column are correct
+# self.assertEqual(list(df['Target Length']), ['Target Length', 3233, 3233, 3233, 3233, 3233, 3233])
+
+# # check that the values in the 'Accessibility Energy' column are correct
+# self.assertEqual(list(df['Accessibility Energy']), ['Accessibility Energy',1.49191, 1.02308, 0.947439, 0.793049, 0.483869, 0.441093])
+
+# # check that the values in the 'Hybridization Energy' column are correct
+# self.assertEqual(list(df['Hybridization Energy']), ['Hybridization Energy',-9.76, -9.76, -9.73, -9.73, -9.73, -9.17])
+
+# # check that the values in the 'Interaction Energy' column are correct
+# self.assertEqual(list(df['Interaction Energy']), ['Interaction Energy',-8.26809, -8.73692, -8.78256, -8.93695, -9.24613, -8.72891])
+
+# # check that the values in the 'BasePair' column are correct
+# self.assertEqual(list(df['BasePair']), ['BasePair','(0-14:2988-2974)', '(0-14:18-4)', '(0-14:17-3)', '(0-14:16-2)', '(0-14:15-1)', '(0-14:14-0)'])