diff scripts/functions.py @ 2:988467f963f0 draft

planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/functions.py	Wed Jan 17 08:57:49 2018 -0500
@@ -0,0 +1,41 @@
+def simplify_fasta_name(fasta_name,LT):
+    for abbreviation in LT:
+        if abbreviation in fasta_name:
+            new_fasta_name = abbreviation
+
+    return(new_fasta_name)
+
+## Generates bash, with key = fasta name; value = sequence (WITH GAP, IF ANY, REMOVED IN THIS FUNCTION)
+def dico(fasta_file,LT):
+
+    count_fastaName=0
+    F1 = open(fasta_file, "r")
+    
+    bash1 = {}
+    while 1:
+        nextline = F1.readline()
+        #print nextline
+        if not nextline :
+            break
+        
+        if nextline[0] == ">":
+            count_fastaName = count_fastaName + 1
+            fasta_name = nextline[1:-1]
+            nextline = F1.readline()
+            sequence = nextline[:-1]
+            
+            if fasta_name not in bash1.keys():
+                fasta_name = simplify_fasta_name(fasta_name,LT)  ### DEF 0 ###
+                bash1[fasta_name] = sequence
+            else:
+                print fasta_name
+
+    # Find alignment length
+    kk = bash1.keys()
+    key0 = kk[0]
+    seq0 = bash1[key0]
+    ln_seq = len(seq0)
+
+    F1.close()
+    
+    return(bash1)