new file (find N motifs from UniProtKB sequences)

Author: Rahi13

fasta_processor_motif_finder.py

@@ -0,0 +1,43 @@
+#The script parses a fasta file and finds the N glycosylation motif(s) in the protein sequence.
+#The output file produces UniProtKB accession, matched motif and the starting position of the matched motif
+#The script works on fasta file(s) downloaded from UniProtKB. e.g. input file: https://www.uniprot.org/uniprot/P04278.fasta
+
+import re
+
+
+fasta_file = '/Users/rahinavelkar/Desktop/scripts/P04278.fasta'
+outfile = '/Users/rahinavelkar/Desktop/scripts/N_motifs.txt'
+
+
+fh=open(fasta_file)
+
+fasta={}
+counter=0
+
+for line in fh:
+    line=line.rstrip()
+    if line[0]=='>':
+        words=line.split()
+        name=words[0][4:]
+        fasta[name]=''
+    else:
+        fasta[name]= fasta[name]+line
+
+
+for name,seq in fasta.items():
+    pattern = re.finditer('N\wS|N\wT', seq)
+    for i in pattern:
+        if i.group() != 'NPT' and i.group() != 'NPS':
+            motif = i.group()
+            motif_start_pos = i.start()+1
+            sourceFile = open(outfile,'a')
+            print(name, motif, motif_start_pos, file=sourceFile)
+            sourceFile.close()
+    
+        
+
+print('Done')   
+
+
+       
+