diff libs/Initial_functions.py @ 0:6895de35a263 draft

planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/libs/Initial_functions.py	Thu Oct 19 18:16:51 2017 -0400
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+
+def To_list(L):
+  import string
+  New_list=[]
+  for x in L:
+    x1=x[:-1]
+    x1=string.atoi(x1)
+    New_list.append(x1)
+  return New_list
+
+
+def Uniq(L): #return the uniq list and the count number
+  Old=L
+  L.sort()
+  L = [L[i] for i in range(len(L)) if L[i] not in L[:i]]
+  count=[]
+  for j in range(len(L)):
+    y=0
+    for x in Old:
+      if L[j]==x:
+        y+=1
+    count.append(y)
+  return (L,count)
+
+
+def Parse_seros_in_genome_trakr(L): #return the sero names in the sra_result.xlsx, the next step is usually "Uniq" in above 
+  names2=[]
+  for x in L:
+    if "serovar" in x:
+      key_word=x.split("serovar")[1].split("_")[1]  #the seronames
+      if key_word!="str." and key_word!="group": #to eliminate some "serovar_str." and "serovar_group"
+        if key_word in ["I","II","III","IIIa","IIIb","IV","VI","B"]: #the serovar is behind those letters
+          if x.split("serovar")[1].split("_")[2]!="str.":
+            names2.append(x.split("serovar")[1].split("_")[2])
+        else:
+          names2.append(x.split("serovar")[1].split("_")[1])
+  return names2
+
+
+