[GET-dev] GFF3 to Wig ?

Leon Peshkin peshkin at gmail.com
Tue Jan 4 19:10:12 EST 2011 

Hello !
   Could someone point me to a tool which would allow
to create a SAM/BAM file from GFF3 and then export in Wig/BED files.
I thing BAM->BED is possible in bamtools, but how about
GFF3->BAM and BAM->Wig ?
  I am attaching a chunk of my gff3 file - it is alignment of reads
against scaffolds.

thanks !
   -Leon Peshkin


scaffold38913	alignAssembly-sacc454pasa_LV15	cDNA_match	51483	51536	96	+	.	ID=chain_1;Target=GGWHCZS01CVNEB
1 52 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	181791	182015	100	+	.	ID=chain_2;Target=GGWHCZS01B8DBA
8 232 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	182349	182461	98	+	.	ID=chain_2;Target=GGWHCZS01B8DBA
233 345 +
scaffold36953	alignAssembly-sacc454pasa_LV15	cDNA_match	12449	12685	97	-	.	ID=chain_3;Target=GGWHCZS01BYL46
1 241 +
scaffold38915	alignAssembly-sacc454pasa_LV15	cDNA_match	143091	143273	100	+	.	ID=chain_4;Target=GGWHCZS01B68J0
1 183 +
scaffold38408	alignAssembly-sacc454pasa_LV15	cDNA_match	17300	17392	96	-	.	ID=chain_5;Target=GGWHCZS01D8PA1
1 92 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	153548	153684	99	-	.	ID=chain_6;Target=GGWHCZS01BUD6C
8 143 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909581	909657	100	+	.	ID=chain_7;Target=GGWHCZS01B8A85
1 77 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	154234	154314	95	-	.	ID=chain_8;Target=GGWHCZS01EMFO0
1 83 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	153545	153735	98	-	.	ID=chain_8;Target=GGWHCZS01EMFO0
84 275 +
scaffold36409	alignAssembly-sacc454pasa_LV15	cDNA_match	261048	261102	100	+	.	ID=chain_9;Target=GGWHCZS01EUQ0J
1 55 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909591	909657	100	+	.	ID=chain_10;Target=GGWHCZS01DNMTI
1 67 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909602	909657	100	+	.	ID=chain_11;Target=GGWHCZS01CRCLW
1 56 +
scaffold38911	alignAssembly-sacc454pasa_LV15	cDNA_match	143736	143833	98	-	.	ID=chain_12;Target=GGWHCZS01D1K2W
1 98 +
scaffold37916	alignAssembly-sacc454pasa_LV15	cDNA_match	81940	81992	100	+	.	ID=chain_13;Target=GGWHCZS01C6JD5
1 53 +
scaffold37916	alignAssembly-sacc454pasa_LV15	cDNA_match	82836	82926	100	+	.	ID=chain_13;Target=GGWHCZS01C6JD5
54 144 +
scaffold38933	alignAssembly-sacc454pasa_LV15	cDNA_match	135829	135927	98	-	.	ID=chain_14;Target=GGWHCZS01CQ9ZX
1 99 +
scaffold38933	alignAssembly-sacc454pasa_LV15	cDNA_match	134108	134179	95	-	.	ID=chain_14;Target=GGWHCZS01CQ9ZX
100 171 +
scaffold36910	alignAssembly-sacc454pasa_LV15	cDNA_match	94607	94679	97	-	.	ID=chain_15;Target=GGWHCZS01CFNTH
1 71 +
scaffold36910	alignAssembly-sacc454pasa_LV15	cDNA_match	92066	92099	100	-	.	ID=chain_15;Target=GGWHCZS01CFNTH
72 105 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	154234	154314	97	-	.	ID=chain_16;Target=GGWHCZS01DS3UM
1 81 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	153545	153735	100	-	.	ID=chain_16;Target=GGWHCZS01DS3UM
82 272 +
scaffold36953	alignAssembly-sacc454pasa_LV15	cDNA_match	12449	12683	97	-	.	ID=chain_17;Target=GGWHCZS01CTGNU
1 239 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909592	909664	100	+	.	ID=chain_18;Target=GGWHCZS01CBNFR
1 73 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	154234	154314	98	-	.	ID=chain_19;Target=GGWHCZS01CR372
1 81 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	153545	153735	100	-	.	ID=chain_19;Target=GGWHCZS01CR372
82 272 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909588	909667	97	+	.	ID=chain_20;Target=GGWHCZS01DOL8E
1 80 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	182394	182451	98	+	.	ID=chain_21;Target=GGWHCZS01E37KQ
1 58 +
scaffold36407	alignAssembly-sacc454pasa_LV15	cDNA_match	418186	418221	100	+	.	ID=chain_22;Target=GGWHCZS01A7VUK
1 36 +
scaffold36407	alignAssembly-sacc454pasa_LV15	cDNA_match	419038	419166	100	+	.	ID=chain_22;Target=GGWHCZS01A7VUK
37 165 +
scaffold36407	alignAssembly-sacc454pasa_LV15	cDNA_match	419794	419868	100	+	.	ID=chain_22;Target=GGWHCZS01A7VUK
166 240 +
scaffold36421	alignAssembly-sacc454pasa_LV15	cDNA_match	118515	118699	99	-	.	ID=chain_23;Target=GGWHCZS01CJEXS
1 184 +
scaffold37410	alignAssembly-sacc454pasa_LV15	cDNA_match	361706	361809	100	-	.	ID=chain_24;Target=GGWHCZS01BB26P
1 104 +
scaffold37410	alignAssembly-sacc454pasa_LV15	cDNA_match	360904	360952	100	-	.	ID=chain_24;Target=GGWHCZS01BB26P
105 153 +
scaffold37910	alignAssembly-sacc454pasa_LV15	cDNA_match	82980	83092	100	+	.	ID=chain_25;Target=GGWHCZS01DHIW0
1 113 -
scaffold37910	alignAssembly-sacc454pasa_LV15	cDNA_match	83537	83584	94	+	.	ID=chain_25;Target=GGWHCZS01DHIW0
114 163 -
scaffold36430	alignAssembly-sacc454pasa_LV15	cDNA_match	5533	5619	97	-	.	ID=chain_26;Target=GGWHCZS01CINS0
1 89 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	912517	912653	97	-	.	ID=chain_27;Target=GGWHCZS01CY8FF
1 137 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	912168	912225	91	-	.	ID=chain_27;Target=GGWHCZS01CY8FF
138 195 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909589	909659	100	+	.	ID=chain_28;Target=GGWHCZS01CVFMM
1 71 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	154234	154314	100	-	.	ID=chain_29;Target=GGWHCZS01B40FY
1 81 +
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	153547	153735	100	-	.	ID=chain_29;Target=GGWHCZS01B40FY
82 270 +
scaffold36919	alignAssembly-sacc454pasa_LV15	cDNA_match	113299	113345	100	+	.	ID=chain_30;Target=GGWHCZS01DBSZR
1 47 +
scaffold36953	alignAssembly-sacc454pasa_LV15	cDNA_match	12449	12685	97	-	.	ID=chain_31;Target=GGWHCZS01AVC8Y
1 235 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909677	909715	100	+	.	ID=chain_32;Target=GGWHCZS01DC0OZ
1 39 -
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909891	909920	100	+	.	ID=chain_32;Target=GGWHCZS01DC0OZ
40 69 -
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	156139	156176	100	-	.	ID=chain_33;Target=GGWHCZS01CZ1CL
1 38 -
scaffold36419	alignAssembly-sacc454pasa_LV15	cDNA_match	154845	154973	96	-	.	ID=chain_33;Target=GGWHCZS01CZ1CL
39 165 -
scaffold37919	alignAssembly-sacc454pasa_LV15	cDNA_match	122261	122312	96	+	.	ID=chain_34;Target=GGWHCZS01EF1CO
1 51 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909683	909715	100	+	.	ID=chain_35;Target=GGWHCZS01C6B5W
1 33 -
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909891	909915	100	+	.	ID=chain_35;Target=GGWHCZS01C6B5W
34 58 -
scaffold37910	alignAssembly-sacc454pasa_LV15	cDNA_match	266441	266510	98	+	.	ID=chain_36;Target=GGWHCZS01BR14F
1 69 +
scaffold38922	alignAssembly-sacc454pasa_LV15	cDNA_match	137914	137970	100	-	.	ID=chain_37;Target=GGWHCZS01CPA1V
1 57 +
scaffold37917	alignAssembly-sacc454pasa_LV15	cDNA_match	52798	52892	97	-	.	ID=chain_38;Target=GGWHCZS01CMW2K
1 93 +
scaffold36935	alignAssembly-sacc454pasa_LV15	cDNA_match	22274	22398	100	-	.	ID=chain_39;Target=GGWHCZS01C1GEQ
1 125 +
scaffold38911	alignAssembly-sacc454pasa_LV15	cDNA_match	143736	143833	98	-	.	ID=chain_40;Target=GGWHCZS01CAS23
1 98 +
scaffold36433	alignAssembly-sacc454pasa_LV15	cDNA_match	188	343	98	+	.	ID=chain_41;Target=GGWHCZS01D4XLL
1 154 +
scaffold36926	alignAssembly-sacc454pasa_LV15	cDNA_match	91417	91535	100	-	.	ID=chain_42;Target=GGWHCZS01CIJEU
1 119 -
scaffold36926	alignAssembly-sacc454pasa_LV15	cDNA_match	90394	90498	100	-	.	ID=chain_42;Target=GGWHCZS01CIJEU
120 224 -
scaffold38913	alignAssembly-sacc454pasa_LV15	cDNA_match	51431	51614	99	+	.	ID=chain_43;Target=GGWHCZS01DAAC8
1 184 +
scaffold36414	alignAssembly-sacc454pasa_LV15	cDNA_match	498987	499090	98	+	.	ID=chain_44;Target=GGWHCZS01BIZ3D
1 103 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909675	909715	100	+	.	ID=chain_45;Target=GGWHCZS01BLTD9
2 42 -
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909891	909913	100	+	.	ID=chain_45;Target=GGWHCZS01BLTD9
43 65 -
scaffold38913	alignAssembly-sacc454pasa_LV15	cDNA_match	51490	51614	99	+	.	ID=chain_46;Target=GGWHCZS01DCKJA
1 124 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909524	909715	98	+	.	ID=chain_47;Target=GGWHCZS01CSVIX
1 192 -
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909891	909920	100	+	.	ID=chain_47;Target=GGWHCZS01CSVIX
193 222 -
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909602	909659	100	+	.	ID=chain_48;Target=GGWHCZS01D0PFQ
1 58 +
scaffold38416	alignAssembly-sacc454pasa_LV15	cDNA_match	6762	6810	97	+	.	ID=chain_49;Target=GGWHCZS01D0TX7
1 48 +
scaffold38416	alignAssembly-sacc454pasa_LV15	cDNA_match	9003	9119	96	+	.	ID=chain_49;Target=GGWHCZS01D0TX7
49 165 +
scaffold38907	alignAssembly-sacc454pasa_LV15	cDNA_match	833004	833038	97	+	.	ID=chain_50;Target=GGWHCZS01CTCD7
1 34 +
scaffold38907	alignAssembly-sacc454pasa_LV15	cDNA_match	838060	838125	100	+	.	ID=chain_50;Target=GGWHCZS01CTCD7
35 100 +
scaffold38907	alignAssembly-sacc454pasa_LV15	cDNA_match	838570	838591	90	+	.	ID=chain_50;Target=GGWHCZS01CTCD7
101 122 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909608	909720	98	+	.	ID=chain_51;Target=GGWHCZS01B9U4E
1 113 +
scaffold37912	alignAssembly-sacc454pasa_LV15	cDNA_match	387939	388102	98	+	.	ID=chain_52;Target=GGWHCZS01CC4MR
1 163 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909587	909659	100	+	.	ID=chain_53;Target=GGWHCZS01BPMT8
1 73 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	908939	909006	98	+	.	ID=chain_54;Target=GGWHCZS01DPL5E
1 68 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909592	909715	98	+	.	ID=chain_55;Target=GGWHCZS01BHI27
1 124 -
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909891	909920	100	+	.	ID=chain_55;Target=GGWHCZS01BHI27
125 154 -
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	908626	908682	96	+	.	ID=chain_56;Target=GGWHCZS01ED8IJ
1 57 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909603	909659	100	+	.	ID=chain_57;Target=GGWHCZS01BCQYE
1 57 +
scaffold36907	alignAssembly-sacc454pasa_LV15	cDNA_match	249216	249286	97	+	.	ID=chain_58;Target=GGWHCZS01ATA7N
1 69 +
scaffold36414	alignAssembly-sacc454pasa_LV15	cDNA_match	259865	259962	100	-	.	ID=chain_59;Target=GGWHCZS01DYGRT
1 98 +
scaffold38915	alignAssembly-sacc454pasa_LV15	cDNA_match	116917	117033	97	-	.	ID=chain_60;Target=GGWHCZS01BMW8R
1 119 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	911227	911253	100	-	.	ID=chain_61;Target=GGWHCZS01CB12C
1 27 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	910741	910883	97	-	.	ID=chain_61;Target=GGWHCZS01CB12C
28 170 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	910330	910350	100	-	.	ID=chain_61;Target=GGWHCZS01CB12C
171 191 +
scaffold36935	alignAssembly-sacc454pasa_LV15	cDNA_match	40763	40908	100	-	.	ID=chain_62;Target=GGWHCZS01B2SBA
1 146 +
scaffold36935	alignAssembly-sacc454pasa_LV15	cDNA_match	40763	40920	100	-	.	ID=chain_63;Target=GGWHCZS01EHM0P
1 158 +
scaffold37410	alignAssembly-sacc454pasa_LV15	cDNA_match	611218	611305	100	-	.	ID=chain_64;Target=GGWHCZS01BMOMV
1 88 +
scaffold38919	alignAssembly-sacc454pasa_LV15	cDNA_match	102147	102213	100	+	.	ID=chain_65;Target=GGWHCZS01BVMOL
1 67 -
scaffold38919	alignAssembly-sacc454pasa_LV15	cDNA_match	107678	107788	98	+	.	ID=chain_65;Target=GGWHCZS01BVMOL
68 178 -
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909610	909715	97	+	.	ID=chain_66;Target=GGWHCZS01C2HAX
1 107 -
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909891	909920	100	+	.	ID=chain_66;Target=GGWHCZS01C2HAX
108 137 -
scaffold37408	alignAssembly-sacc454pasa_LV15	cDNA_match	16679	16777	98	+	.	ID=chain_67;Target=GGWHCZS01BTFN0
1 98 +
scaffold38932	alignAssembly-sacc454pasa_LV15	cDNA_match	135072	135188	95	-	.	ID=chain_68;Target=GGWHCZS01CURJ7
1 119 +
scaffold37907	alignAssembly-sacc454pasa_LV15	cDNA_match	909586	909657	100	+	.	ID=chain_69;Target=GGWHCZS01CB9IJ
1 72 +
scaffold38911	alignAssembly-sacc454pasa_LV15	cDNA_match	136895	136999	100	+	.	ID=chain_70;Target=GGWHCZS01DBI1M
1 105 +
scaffold38911	alignAssembly-sacc454pasa_LV15	cDNA_match	138219	138319	100	+	.	ID=chain_70;Target=GGWHCZS01DBI1M
106 206 +
scaffold38933	alignAssembly-sacc454pasa_LV15	cDNA_match	135829	135906	97	-	.	ID=chain_71;Target=GGWHCZS01C0GBU
1 77 +
scaffold38933	alignAssembly-sacc454pasa_LV15	cDNA_match	134108	134179	95	-	.	ID=chain_71;Target=GGWHCZS01C0GBU
78 149 +

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