diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/.DS_Store differ
diff --git a/primingsitepredictor/.idea/.gitignore b/primingsitepredictor/.idea/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..13566b81b018ad684f3a35fee301741b2734c8f4
--- /dev/null
+++ b/primingsitepredictor/.idea/.gitignore
@@ -0,0 +1,8 @@
+# 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
new file mode 100644
index 0000000000000000000000000000000000000000..105ce2da2d6447d11dfe32bfb846c3d5b199fc99
--- /dev/null
+++ b/primingsitepredictor/.idea/inspectionProfiles/profiles_settings.xml
@@ -0,0 +1,6 @@
+<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
new file mode 100644
index 0000000000000000000000000000000000000000..e6a7aa474cd32e70c4d9694c40996d01e47c23fc
--- /dev/null
+++ b/primingsitepredictor/.idea/misc.xml
@@ -0,0 +1,4 @@
+<?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
new file mode 100644
index 0000000000000000000000000000000000000000..b7f52b9584a9cd9443097c0f753a17a344fa41a0
--- /dev/null
+++ b/primingsitepredictor/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?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
new file mode 100644
index 0000000000000000000000000000000000000000..d0876a78d06ac03b5d78c8dcdb95570281c6f1d6
--- /dev/null
+++ b/primingsitepredictor/.idea/primingsitepredictor.iml
@@ -0,0 +1,8 @@
+<?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
new file mode 100644
index 0000000000000000000000000000000000000000..6c0b8635858dc7ad44b93df54b762707ce49eefc
--- /dev/null
+++ b/primingsitepredictor/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?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
index 545f1100114ec5eb992d22bc71d364b8663a7638..251777b9e4a409e7bb32d851b7bee98032bd3d6c 100644
--- a/primingsitepredictor/Primer1.fasta
+++ b/primingsitepredictor/Primer1.fasta
@@ -1,2 +1,2 @@
-<primer1
-TTTTTTTTTTTTTTT
+<primer1
+TTTTTTTTTTTTTTT
diff --git a/primingsitepredictor/cli.py b/primingsitepredictor/cli.py
index 5b665962b5b9b5aa698793c7fe4e3d4cba2db16f..218fbb65b4c66ea098d317a17bbee015706d4933 100644
--- a/primingsitepredictor/cli.py
+++ b/primingsitepredictor/cli.py
@@ -1,35 +1,36 @@
# -*- coding: utf-8 -*-
"""
-Created on Mon Nov 14 14:49:50 2022
+Changed on Fr Dec 23 16:49:50 2022
-@author: baerma
+@author: RobinC
"""
import argparse
import logging
import main
-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',
- epilog = 'To predict or not to predict')
- parser.add_argument('energycutoff', type=float, help='a float as energy Cutoff')
- #parser.add_argument('transcripts', help='fastafile containing transcripts') #What type is that? fasta? Actually doesn't make sense here
- args = parser.parse_args()
- energy_cutoff = args.energycutoff
- return energy_cutoff
-#possibly make a class out of this although I think it's an overkill
+class CLI():
+ def create_parser(self):
+ """This function creates the parser"""
-def letsgo():
- energy_cutoff = create_parser()
- print(f"Your energy cutoff is {energy_cutoff}")
+ 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__':
logging.basicConfig(
format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
level=logging.INFO,
- )
+ )
LOG = logging.getLogger(__name__)
main()
- #here we would point to the main module and parse the energy cutoff
+
diff --git a/primingsitepredictor/createprimer.py b/primingsitepredictor/createprimer.py
index c2c234f2eca3c07dd400098897f2586ceb0a7183..8dcd2329f74f6f0c6254ff428dd323aa9bf8fe53 100644
--- a/primingsitepredictor/createprimer.py
+++ b/primingsitepredictor/createprimer.py
@@ -1,8 +1,8 @@
# -*- coding: utf-8 -*-
"""
-Created on Wed Nov 16 14:17:06 2022
+Changed on Fr Dec 23 14:34:20 2022
-@author: baerma
+@author: RobinC
"""
class CreatePrimer:
@@ -13,8 +13,7 @@ class CreatePrimer:
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:
diff --git a/primingsitepredictor/main.py b/primingsitepredictor/main.py
index 07348dd4b21c73c4a8be7d07a2f351e1cab7fd5f..d8d80b1e26440880da3aaacd2ffa336ebe0a95cf 100644
--- a/primingsitepredictor/main.py
+++ b/primingsitepredictor/main.py
@@ -1,10 +1,16 @@
+"""
+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()
- create_gtf()
+
def generate_RIBlast_input():
@@ -20,9 +26,5 @@ def create_gtf():
gtf_file = PostProcessRIBlast().output
print(gtf_file)
-
-
-main()
-
if __name__ == '__main__':
main()
diff --git a/primingsitepredictor/my_primer.fasta b/primingsitepredictor/my_primer.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..70ef81c7f1201827c1886f6cf15efec0ec65ecf3
--- /dev/null
+++ b/primingsitepredictor/my_primer.fasta
@@ -0,0 +1,2 @@
+<my_primer
+TTTTTTTTTTTTTTTTTTTT
diff --git a/primingsitepredictor/output_transcripts_df.GTF b/primingsitepredictor/output_transcripts_df.GTF
new file mode 100644
index 0000000000000000000000000000000000000000..89ba6f367701e787b727d3602c241853c88d61d8
--- /dev/null
+++ b/primingsitepredictor/output_transcripts_df.GTF
@@ -0,0 +1,33 @@
+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/output_transcripts_df.txt b/primingsitepredictor/output_transcripts_df.txt
index bb43f201dfc4ff5c44ff9de6b45d5dfe82799c18..89ba6f367701e787b727d3602c241853c88d61d8 100644
--- a/primingsitepredictor/output_transcripts_df.txt
+++ b/primingsitepredictor/output_transcripts_df.txt
@@ -1,3 +1,33 @@
-Transcript_1 RIBlast Priming_site 2974 2988 . + . Accessibility_Energy "0.08051396365277928"
-Transcript_1 RIBlast Priming_site 4 18 . + . Accessibility_Energy "0.17770481173297115"
-Transcript_2 RIBlast Priming_site 1270 1284 . + . Accessibility_Energy "0.6445369481689498"
+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
index 125950e493a8399cf4297eeb0778ca531325dc2a..e2504e0f98e7a6527f508715d018aace78066c5c 100644
--- a/primingsitepredictor/postprocessing.py
+++ b/primingsitepredictor/postprocessing.py
@@ -60,15 +60,10 @@ class PostProcessRIBlast():
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')
-<<<<<<< HEAD
- with open('output_transcripts_df.txt', 'w') as f:
+ with open('output_transcripts_df.GTF', 'w') as f:
f.write(self.output)
-
+ return(self.output)
-=======
- return(self.output)
->>>>>>> 9d8e928323a99c5e86557c4b53ab93aaf8f5beb5
-
-#print(PostProcessRIBlast().output)
\ No newline at end of file
+print(PostProcessRIBlast().output)
\ No newline at end of file
diff --git a/primingsitepredictor/test/RIBlast output example.txt b/primingsitepredictor/test/RIBlast output example.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3a270893926da9f8b302af5b15dbed875a6475f
--- /dev/null
+++ b/primingsitepredictor/test/RIBlast output example.txt
@@ -0,0 +1,37 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/primingsitepredictor/test/output_transcripts_df.GTF b/primingsitepredictor/test/output_transcripts_df.GTF
new file mode 100644
index 0000000000000000000000000000000000000000..89ba6f367701e787b727d3602c241853c88d61d8
--- /dev/null
+++ b/primingsitepredictor/test/output_transcripts_df.GTF
@@ -0,0 +1,33 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..89ba6f367701e787b727d3602c241853c88d61d8
--- /dev/null
+++ b/primingsitepredictor/test/output_transcripts_df.txt
@@ -0,0 +1,33 @@
+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/primer1.fasta b/primingsitepredictor/test/primer1.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..251777b9e4a409e7bb32d851b7bee98032bd3d6c
--- /dev/null
+++ b/primingsitepredictor/test/primer1.fasta
@@ -0,0 +1,2 @@
+<primer1
+TTTTTTTTTTTTTTT
diff --git a/primingsitepredictor/test/test_cli.py b/primingsitepredictor/test/test_cli.py
new file mode 100644
index 0000000000000000000000000000000000000000..dec66a1765914a96fbb354b33bcbbd07694833a7
--- /dev/null
+++ b/primingsitepredictor/test/test_cli.py
@@ -0,0 +1,103 @@
+"""
+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
new file mode 100644
index 0000000000000000000000000000000000000000..a54ad9c01245b741d89346851b1b3a7c76ff726d
--- /dev/null
+++ b/primingsitepredictor/test/test_createprimer.py
@@ -0,0 +1,71 @@
+"""
+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_fasta.fasta b/primingsitepredictor/test/test_fasta.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..5b85943f52a87f58f84c34e9c994e97c2f5a4e9a
--- /dev/null
+++ b/primingsitepredictor/test/test_fasta.fasta
@@ -0,0 +1,2 @@
+ATGC
+CAGT
diff --git a/primingsitepredictor/test/test_main.py b/primingsitepredictor/test/test_main.py
new file mode 100644
index 0000000000000000000000000000000000000000..1ac3d3c6f6f77b3a7945be939347c7536357d633
--- /dev/null
+++ b/primingsitepredictor/test/test_main.py
@@ -0,0 +1,93 @@
+"""
+Created on Tue Dec 20 14:06:20 2022
+
+@author: RobinC
+"""
+
+# Imports
+import os, sys
+currentdir = os.path.dirname(os.path.realpath(__file__))
+parentdir = os.path.dirname(currentdir)
+sys.path.append(parentdir)
+import unittest
+import main as mn
+import createprimer as cp
+import postprocessing as pp
+from io import StringIO
+
+class TestMain(unittest.TestCase):
+
+ def test_import(self):
+ """Test function for module imports"""
+ try:
+ import CreatePrimer
+ except ImportError:
+ self.fail("Failed to import CreatePrimer")
+
+ try:
+ import PostProcessRIBlast
+ except ImportError:
+ self.fail("Failed to import PostProcessRIBlast")
+
+ 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()
+ primer.create_fasta()
+
+ # get the name and the transcript filename
+ primer_filename = primer.name+".fasta"
+ transcript_filename = "transcripts.fasta"
+
+ # Call the generate_RIBlast_input() method
+ result = mn.generate_RIBlast_input()
+
+ assert result == [primer_filename, transcript_filename]
+
+
+ def test_create_gtf(self):
+ """Test funciton for the method create_gtf()"""
+
+ # Call the output of the PostprocessRIBlast() method
+ result = pp.PostProcessRIBlast().output
+
+ # Open the expected output
+ with open('output_transcripts_df.txt', 'r') as f:
+ expected_output = f.read()
+
+ # Use an assertion to check the output result
+ assert result == expected_output
+
+ # Capture the output of the print statement
+ captured_output = StringIO()
+ sys.stdout = captured_output
+
+ # Call the function that contains the print statement
+ mn.create_gtf()
+
+ # Check the captured output against the expected value
+ assert captured_output.getvalue().strip() == expected_output
+
+
+ def test_main(self):
+ """Test function for the method main()"""
+
+ # Call the CreatePrimer() method and the create_fasta() method
+ primer = cp.CreatePrimer()
+ primer.create_fasta()
+
+ # get the name and the transcript filename
+ primer_filename = primer.name+".fasta"
+ transcripts_filename = "transcripts.fasta"
+
+ # Get the results for the called methods
+ result1 = mn.generate_RIBlast_input()
+ result2 = mn.create_gtf()
+
+ # Open the expected output
+ with open('output_transcripts_df.txt', 'r') as f:
+ expected_output = f.read()
+
+ assert result1 == [primer_filename, transcripts_filename]
+ assert result2 == expected_output
diff --git a/primingsitepredictor/test/test_postprocessing.py b/primingsitepredictor/test/test_postprocessing.py
new file mode 100644
index 0000000000000000000000000000000000000000..2948ef269fe44e369cd619e63ab930608e03dc8e
--- /dev/null
+++ b/primingsitepredictor/test/test_postprocessing.py
@@ -0,0 +1,157 @@
+"""
+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
new file mode 100644
index 0000000000000000000000000000000000000000..5b85943f52a87f58f84c34e9c994e97c2f5a4e9a
--- /dev/null
+++ b/primingsitepredictor/test_fasta.fasta
@@ -0,0 +1,2 @@
+ATGC
+CAGT