# HG changeset patch
# User yating-l
# Date 1483138254 18000
# Node ID 148e353417e79ceb71cfd59d61179c0d6e865760
# Parent  1a0e39acb62f231423e2a66685f79b336ba9059c
planemo upload commit af6c4dc7f6d6795f2b2db7299eb14ae1d5622ac1

diff -r 1a0e39acb62f -r 148e353417e7 rename.py
--- a/rename.py	Mon Dec 19 17:14:55 2016 -0500
+++ b/rename.py	Fri Dec 30 17:50:54 2016 -0500
@@ -14,13 +14,17 @@
                 if ">" in line:
                     oldname = line[1:].rstrip()
                     newname = "scaffold_" + str(i)
-                    line = ">" + newname + "\n"
+                    line = ">" + newname
                     i = i+1
                     namemap[oldname] = newname
-                out.write(line)
+                #TODO: Add line breaks to chromosome sequences that are in a single line
+                #else:
+                    #if (len(line) > 50):
+                        #for 
+                out.write(line.rstrip() + "\n")
     with open(indexfile, 'w') as index:
         for k in namemap:
-            index.write(k + "=>" + namemap[k] + "\n")
+            index.write(k + "\t" + namemap[k] + "\n")
 
 def main():
     inputfile = str(sys.argv[1])
diff -r 1a0e39acb62f -r 148e353417e7 test-data/Dbia3_index.fa
--- a/test-data/Dbia3_index.fa	Mon Dec 19 17:14:55 2016 -0500
+++ b/test-data/Dbia3_index.fa	Fri Dec 30 17:50:54 2016 -0500
@@ -1,70 +1,70 @@
-contig1=>scaffold_1
-contig2=>scaffold_2
-contig3=>scaffold_3
-contig4=>scaffold_4
-contig5=>scaffold_5
-contig6=>scaffold_6
-contig7=>scaffold_7
-contig8=>scaffold_8
-contig9=>scaffold_9
-contig10=>scaffold_10
-contig11=>scaffold_11
-contig12=>scaffold_12
-contig13=>scaffold_13
-contig14=>scaffold_14
-contig15=>scaffold_15
-contig16=>scaffold_16
-contig17=>scaffold_17
-contig18=>scaffold_18
-contig19=>scaffold_19
-contig20=>scaffold_20
-contig21=>scaffold_21
-contig22=>scaffold_22
-contig23=>scaffold_23
-contig24=>scaffold_24
-contig25=>scaffold_25
-contig26=>scaffold_26
-contig27=>scaffold_27
-contig28=>scaffold_28
-contig29=>scaffold_29
-contig30=>scaffold_30
-contig31=>scaffold_31
-contig32=>scaffold_32
-contig33=>scaffold_33
-contig34=>scaffold_34
-contig35=>scaffold_35
-contig36=>scaffold_36
-contig37=>scaffold_37
-contig38=>scaffold_38
-contig39=>scaffold_39
-contig40=>scaffold_40
-contig41=>scaffold_41
-contig42=>scaffold_42
-contig43=>scaffold_43
-contig44=>scaffold_44
-contig45=>scaffold_45
-contig46=>scaffold_46
-contig47=>scaffold_47
-contig48=>scaffold_48
-contig49=>scaffold_49
-contig50=>scaffold_50
-contig51=>scaffold_51
-contig52=>scaffold_52
-contig53=>scaffold_53
-contig54=>scaffold_54
-contig55=>scaffold_55
-contig56=>scaffold_56
-contig57=>scaffold_57
-contig58=>scaffold_58
-contig59=>scaffold_59
-contig60=>scaffold_60
-contig61=>scaffold_61
-contig62=>scaffold_62
-contig63=>scaffold_63
-contig64=>scaffold_64
-contig65=>scaffold_65
-contig66=>scaffold_66
-contig67=>scaffold_67
-contig68=>scaffold_68
-contig69=>scaffold_69
-contig70=>scaffold_70
+contig1	scaffold_1
+contig2	scaffold_2
+contig3	scaffold_3
+contig4	scaffold_4
+contig5	scaffold_5
+contig6	scaffold_6
+contig7	scaffold_7
+contig8	scaffold_8
+contig9	scaffold_9
+contig10	scaffold_10
+contig11	scaffold_11
+contig12	scaffold_12
+contig13	scaffold_13
+contig14	scaffold_14
+contig15	scaffold_15
+contig16	scaffold_16
+contig17	scaffold_17
+contig18	scaffold_18
+contig19	scaffold_19
+contig20	scaffold_20
+contig21	scaffold_21
+contig22	scaffold_22
+contig23	scaffold_23
+contig24	scaffold_24
+contig25	scaffold_25
+contig26	scaffold_26
+contig27	scaffold_27
+contig28	scaffold_28
+contig29	scaffold_29
+contig30	scaffold_30
+contig31	scaffold_31
+contig32	scaffold_32
+contig33	scaffold_33
+contig34	scaffold_34
+contig35	scaffold_35
+contig36	scaffold_36
+contig37	scaffold_37
+contig38	scaffold_38
+contig39	scaffold_39
+contig40	scaffold_40
+contig41	scaffold_41
+contig42	scaffold_42
+contig43	scaffold_43
+contig44	scaffold_44
+contig45	scaffold_45
+contig46	scaffold_46
+contig47	scaffold_47
+contig48	scaffold_48
+contig49	scaffold_49
+contig50	scaffold_50
+contig51	scaffold_51
+contig52	scaffold_52
+contig53	scaffold_53
+contig54	scaffold_54
+contig55	scaffold_55
+contig56	scaffold_56
+contig57	scaffold_57
+contig58	scaffold_58
+contig59	scaffold_59
+contig60	scaffold_60
+contig61	scaffold_61
+contig62	scaffold_62
+contig63	scaffold_63
+contig64	scaffold_64
+contig65	scaffold_65
+contig66	scaffold_66
+contig67	scaffold_67
+contig68	scaffold_68
+contig69	scaffold_69
+contig70	scaffold_70