Resolve FlyBase genome annotations for same family with multiple names

[cbergman]

Several TEs in Release 6.10 have different instances annotated with different names for the same TE family. One of these (aurora-element/ninja-Dsim-like) has been discussed in #24. First attempt at compiling list of families with annotations that need change to symbol:

aurora -> aurora-element
DM88 -> Dm88
Doc2 -> Doc2-element
Doc3 -> Doc3-element
G -> G-element
R1A1 -> R1A1-element
X -> X-element
ninja-Dsim-like -> aurora-element

• list obtained by quick extraction of symbols in FBti IDs, as follows:

$ wget ftp://ftp.flybase.net/releases/FB2016_02/dmel_r6.10/gff/dmel-all-r6.10.gff.gz
$ zcat dmel-all-r6.10.gff.gz | grep FBti | grep -v 'P{' | grep -v PBac | grep -v 'Mi{' | grep -v sim4 | cut -f 9 | cut -f 2 -d ";" | cut -f 2 -d '=' | cut -f 1 -d '{' | sort | uniq -c
     18 ?
    303 1360
     13 1731
     21 17.6
     80 297
     17 3S18
     52 412
      2 422
      3 accord
      7 accord2
      1 aurora
     34 baggins
      6 Bari1
      5 Bari2
     29 blood
     43 BS
     29 BS3
      1 BS4
     22 Burdock
      5 Circe
     39 copia
    152 Cr1a
      1 CR32010
      1 Delta88
     11 diver
     47 diver2
     29 Dm88
      2 DM88
     77 Doc
      6 Doc2
      1 Doc2-element
     16 Doc3
      5 Doc3-element
      7 Doc4
     74 F
     62 FB
     30 flea
      2 frogger
      9 Fw2
      7 Fw3
     17 G
     21 G2
      7 G3
     28 G4
     25 G5
     27 G5A
     10 G6
      4 G7
     18 GATE
     19 gtwin
     23 gypsy
      7 gypsy10
      5 gypsy11
     50 gypsy12
     12 gypsy2
     15 gypsy3
     15 gypsy4
     10 gypsy5
     15 gypsy6
      4 gypsy7
     56 gypsy8
     10 gypsy9
     69 H
     60 HB
      9 Helena
      2 Herm
     26 HeT-A
     23 HeT-Tag
     25 HMS-Beagle
     12 HMS-Beagle2
     25 hopper
     14 hopper2
     41 I
     17 Idefix
   2234 INE-1
     45 invader1
     19 invader2
     33 invader3
     32 invader4
      3 invader5
      8 invader6
     11 Ivk
     97 jockey
     28 jockey2
     11 Juan
      1 kibra
      4 looper1
      3 M
     23 mariner2
     21 Max
      8 McClintock
     40 mdg1
     22 mdg3
     13 micropia
     17 ninja-Dsim-like
      8 NOF
     36 opus
     48 pogo
      7 Porto1
      5 Q
     29 Quasimodo
      2 R1-2
     26 R1A1
      1 roamer
    156 roo
     17 rooA
      8 rover
     25 Rt1a
     58 Rt1b
     33 Rt1c
     65 S
     14 S2
     28 springer
     20 Stalker
     17 Stalker2
      1 Stalker3
     37 Stalker4
      9 Tabor
     10 TART-A
      3 TART-B
      1 TART-C
     26 Tc1
     24 Tc1-2
     19 Tc3
     27 Tirant
     28 Tol2
      4 Tom1
      3 transib1
     24 transib2
     13 transib3
      8 transib4
      6 Transpac
     55 X
      1 Xanthias
      4 Y
      4 ZAM

• note: not all of above are valid TEs (Y, kibra)