ClusterMC

A clustering program that accepts and validates users input.

Utilities/for_fastas/ClusterMC_Feb9.py

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+#Professor L. Katz and Godwin Ani
+#9th- Feb- 2023
+#A clustering program that accepts and validates users input
+
+import os, sys, re
+from tqdm import tqdm
+
+
+def cluster():
+    ''' This function takes an amino acid or DNA sequence stored in a fasta format and clusters it.
+It uses two nested functions (cluster_AA and cluster_DNA) to perform this operation.
+Ensure that fasta files to be clustered are stored in a root directory folder named "to_cluster". This folder will automatically be created if none exists.
+The result of the clustering process is saved into a root directory folder named "Clustered" which is created automatically if none exists. '''
+  
+    if not os.path.isdir('to_cluster'):
+        os.mkdir('to_cluster')
+        
+    if not os.path.isdir('Clustered'):
+        os.mkdir('Clustered')
+    # Nested function for amino acids clustering.    
+    def cluster_AA():
+    #input validation for the sequence identity threshold.
+        while True:
+            try:
+                val1 =input( 'Amino Acids Sequence Identity Threshold (e.g. 0.99, 0.95)? : ')
+                integer, fractional = val1.split('.')
+                val1 = float(val1)
+                if int(integer)== 0 and len(fractional) == 2:
+                    break
+            except ValueError:
+                pass
+            print('ERROR! Use format 0.## for Amino acids sequence identity threshold.')
+ 
+      #Input validation for the overlap value.
+        while True:
+            try:
+                val2 =input( 'Amino Acids Alignment Overlap Value (e.g. 0.67, 0.75)? : ')
+                integer, fractional = val2.split('.')
+                val2 = float(val2)
+                if int(integer)== 0 and len(fractional) == 2:
+                    break
+            except ValueError:
+                pass
+            print('ERROR! Use format 0.## for Amino acids sequence alignment overlap value')
+            
+  #Selects amino acids fasta files in "to_cluster" folder and clusters them with CD-HIT.
+        for file in tqdm(os.listdir('to_cluster')):
+            if file.endswith('.fasta'):
+                os.system('cd-hit -i to_cluster/' + file + ' -o Clustered/' + file + ' -c %s -d 0 -aS %s' %( val1, val2))
+     #Renaming the result of the clustering.
+        for file in os.listdir('Clustered'):
+            if file.endswith('.clstr'):
+                os.rename('Clustered/' + file, 'Clustered/' + file.split('FILE')[0] + 'Clustered.txt')
+
+
+    #Nested function for DNA clustering.
+    def cluster_DNA():
+        #Input validation for the sequence identity threshold.
+        while True:
+            try:
+                val1 =input( 'DNA Sequence Identity Threshold (e.g. 0.99, 0.95)? : ')
+                integer, fractional = val1.split('.')
+                val1 = float(val1)
+                if int(integer)== 0 and len(fractional) == 2:
+                    break
+            except ValueError:
+                pass
+            print('ERROR! Use format 0.## for DNA sequence identity threshold.')
+      #Input validation for the overlap value. 
+        while True:
+            try:
+                val2 =input( 'DNA Sequence Alignment Overlap Value (e.g. 0.67, 0.75)? : ')
+                integer, fractional = val2.split('.')
+                val2 = float(val2)
+                if int(integer)== 0 and len(fractional) == 2:
+                    break
+            except ValueError:
+                pass
+            print('ERROR! Use format 0.## for DNA sequence alignment overlap value.')
+            
+            #Selects DNA fasta files in "to_cluster" folder and clusters them with CD-HIT.
+        for file in tqdm(os.listdir('to_cluster')):
+            if file.endswith('.fasta'):
+                os.system('cd-hit-est -i to_cluster/' + file + ' -o Clustered/' + file + ' -c %s -d 0 -aS %s' %( val1, val2))
+
+        #Renaming the result of the clustering.
+        for file in os.listdir('Clustered'):
+            if file.endswith('.clstr'):
+                os.rename('Clustered/' + file, 'Clustered/' + file.split('FILE')[0] + 'Clustered.txt')
+
+    # Prompts for user input and function call.
+    choice_1 = input('Are you clustering Amino Acids or DNA? (AA or DNA) : ')
+    if choice_1 in ['AA', 'Aa', 'aa']:
+        cluster_AA()
+    elif choice_1 in ['DNA', 'Dna', 'dna']:
+        cluster_DNA()
+    else:
+        print('Sorry. This program can only cluster Amino Acids and DNA')
+
+cluster()
+