Select the main accessions removing isoform information from fasta file.

Stripping the keyword for the xml file if has some space in the begining of the line.

XML_Subsetter/extract_uniprot_XML.py

@@ -47,9 +47,6 @@
 
 
 import re
-import sys
-import getopt
-
 
 
 def define_db(database):
@@ -107,6 +104,9 @@ if isFasta:
     for line in lines:
         if line.startswith(">"):
             acc=line.split("|")[1]
+            if acc.find("-"):
+                acc=acc.split("-")[0]
+                print(acc)
             l_acc.append(acc)
     print("\n")        
     print("Number of sequence in fasta file: "+str(len(l_acc))+"\n")
@@ -116,6 +116,8 @@ else:
     print("\n")        
     print("Number of accessions in file: "+str(len(l_acc))+"\n")
 
+l_acc = list(dict.fromkeys(l_acc))
+
 
 
 xmlo=open(options.output_name+".xml","w")
@@ -130,7 +132,7 @@ flag_entry=0
 temp_entry=[]
 toprint=1
 for line in xml_lines:
-    if line.startswith("<entry"):
+    if line.strip().startswith("<entry"):
         acc=[]
         seq=[]
         name=""
@@ -139,21 +141,21 @@ for line in xml_lines:
         temp_entry=[line]
         flag_entry=1
         toprint=1
-    elif line.startswith("<accession"):
+    elif line.strip().startswith("<accession"):
         acc.append(re.split(">|<",line)[2])
         temp_entry.append(line)
-    elif line.startswith("<sequence"):
+    elif line.strip().startswith("<sequence"):
         temp_entry.append(line)
         if line.find("</sequence>"):
             seq=re.split(">|<",line)[2]
-    elif line.startswith("<name>"):
+    elif line.strip().startswith("<name>"):
         temp_entry.append(line)
         name=re.split(">|<",line)[2]
-    elif line.startswith("<fullName>"):
+    elif line.strip().startswith("<fullName>"):
         temp_entry.append(line)
         if fullname=="":
             fullname=re.split(">|<",line)[2]
-    elif line.startswith('</entry'):
+    elif line.strip().startswith('</entry'):
         temp_entry.append(line)
         flag_entry=0
         # we test if we have to keep this proteoform