git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@80 60f365c0-8329-0410-b2a4-ec073aeeaa1d

tools/ecoPCRFormat.py

@@ -294,25 +294,25 @@ def emblEntryParser(entry):
 
 ######################
 
-_fastaParseID = re.compile('(?<=^>)[^ ]+')
-_fastaParseDE = re.compile('(?<=^>).+',)   
-_fastaParseSQ = re.compile('^[^>].+',re.MULTILINE+re.DOTALL)
-_fastaParseTX = re.compile('(?<=[[Tt]axon:) *[0-9]+ *(?=])')
+def parseFasta(seq):
+    title = seq[0].strip()[1:].split(None,1)
+    id=title[0]
+    if len(title) == 2:
+        field = title[1].split('; ')
+    else:
+        field=[]
+    info = dict(x.split('=') for x in field if '=' in x)
+    definition = ' '.join([x for x in field if '=' not in x])
+    seq=(''.join([x.strip() for x in seq[1:]])).upper()
+    return id,seq,definition,info
+
   
 def fastaEntryParser(entry):
-    Id = _fastaParseID.findall(entry)[0]
-    De = _fastaParseDE.findall(entry)[0].split(None,1)[1:]
-    if not De:
-        De=''
-    else:
-        De=De[0]
-    Sq = cleanSeq(_fastaParseSQ.findall(entry)[0].upper())  
-    try:
-        Tx = int(_fastaParseTX.findall(entry)[0])
-    except IndexError:
-        Tx = None
-          
-    return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
+    id,seq,definition,info = parseFasta(entry)
+    Tx = info.get('taxid',None)   
+    if Tx is not None:
+        Tx=int(Tx)
+    return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}