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Full Discussion: Awk script
Top Forums Shell Programming and Scripting Awk script Post 302498293 by shen on Monday 21st of February 2011 01:34:39 AM
Old 02-21-2011
Here is the expected input and output,but your code not generate following output
Code:
sscaffold_1	phytozome6	gene	12632	13612	.	+	.	ID=POPTR_0001s00200;Name=POPTR_0001s00200
scaffold_1	phytozome6	mRNA	12632	13612	.	+	.	ID=PAC:18235173;Name=POPTR_0001s00200.1;PACid=18235173;Parent=POPTR_0001s00200
scaffold_1	phytozome6	5'-UTR	12632	12638	.	+	.	Parent=PAC:18235173;PACid=18235173
scaffold_1	phytozome6	CDS	12639	12650	.	+	0	Parent=PAC:18235173;PACid=18235173
scaffold_1	phytozome6	CDS	12768	12891	.	+	0	Parent=PAC:18235173;PACid=18235173
scaffold_1	phytozome6	CDS	13117	13226	.	+	2	Parent=PAC:18235173;PACid=18235173
scaffold_1	phytozome6	CDS	13310	13384	.	+	0	Parent=PAC:18235173;PACid=18235173
scaffold_1	phytozome6	3'-UTR	13385	13612	.	+	.	Parent=PAC:18235173;PACid=18235173
scaffold_1	phytozome6	gene	19769	22804	.	+	.	ID=POPTR_0001s00210;Name=POPTR_0001s00210
scaffold_1	phytozome6	mRNA	19769	22804	.	+	.	ID=PAC:18238552;Name=POPTR_0001s00210.1;PACid=18238552;Parent=POPTR_0001s00210
scaffold_1	phytozome6	5'-UTR	19769	19827	.	+	.	Parent=PAC:18238552;PACid=18238552
scaffold_1	phytozome6	CDS	19828	20136	.	+	0	Parent=PAC:18238552;PACid=18238552
scaffold_1	phytozome6	CDS	22190	22516	.	+	0	Parent=PAC:18238552;PACid=18238552
scaffold_1	phytozome6	3'-UTR	22517	22804	.	+	.	Parent=PAC:18238552;PACid=18238552
scaffold_1	phytozome6	gene	74076	75893	.	+	.	ID=POPTR_0001s00220;Name=POPTR_0001s00220
scaffold_1	phytozome6	mRNA	74076	75893	.	+	.	ID=PAC:18237390;Name=POPTR_0001s00220.1;PACid=18237390;Parent=POPTR_0001s00220
scaffold_1	phytozome6	CDS	74076	74235	.	+	0	Parent=PAC:18237390;PACid=18237390
scaffold_1	phytozome6	CDS	74359	74634	.	+	2	Parent=PAC:18237390;PACid=18237390
scaffold_1	phytozome6	CDS	75259	75893	.	+	2	Parent=PAC:18237390;PACid=18237390
scaffold_1	phytozome6	gene	80191	81289	.	-	.	ID=POPTR_0001s00230;Name=POPTR_0001s00230
scaffold_1	phytozome6	mRNA	80191	81289	.	-	.	ID=PAC:18235601;Name=POPTR_0001s00230.1;PACid=18235601;Parent=POPTR_0001s00230
scaffold_1	phytozome6	CDS	81161	81289	.	-	0	Parent=PAC:18235601;PACid=18235601
scaffold_1	phytozome6	CDS	80191	80385	.	-	0	Parent=PAC:18235601;PACid=18235601

desired output
Code:
scaffold_1	phytozome6	gene	12632	13612	.	+	.	ID=POPTR_0001s00200;Name=POPTR_0001s00200
scaffold_1	phytozome6	mRNA	12632	13612	.	+	.	ID=POPTR_0001s00200.1;Name=POPTR_0001s00200.1;PACid=18235173;Parent=POPTR_0001s00200
scaffold_1	phytozome6	5'-UTR	12632	12638	.	+	.	Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1	phytozome6	CDS	12639	12650	.	+	0	Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1	phytozome6	CDS	12768	12891	.	+	0	Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1	phytozome6	CDS	13117	13226	.	+	2	Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1	phytozome6	CDS	13310	13384	.	+	0	Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1	phytozome6	3'-UTR	13385	13612	.	+	.	Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1	phytozome6	gene	19769	22804	.	+	.	ID=POPTR_0001s00210;Name=POPTR_0001s00210
scaffold_1	phytozome6	mRNA	19769	22804	.	+	.	ID=POPTR_0001s00210.1;Name=POPTR_0001s00210.1;PACid=18238552;Parent=POPTR_0001s00210
scaffold_1	phytozome6	5'-UTR	19769	19827	.	+	.	Parent=POPTR_0001s00210.1;PACid=18238552
scaffold_1	phytozome6	CDS	19828	20136	.	+	0	Parent=POPTR_0001s00210.1;PACid=18238552
scaffold_1	phytozome6	CDS	22190	22516	.	+	0	Parent=POPTR_0001s00210.1;PACid=18238552
scaffold_1	phytozome6	3'-UTR	22517	22804	.	+	.	Parent=POPTR_0001s00210.1;PACid=18238552
scaffold_1	phytozome6	gene	74076	75893	.	+	.	ID=POPTR_0001s00220;Name=POPTR_0001s00220
scaffold_1	phytozome6	mRNA	74076	75893	.	+	.	ID=POPTR_0001s00220.1;Name=POPTR_0001s00220.1;PACid=18237390;Parent=POPTR_0001s00220
scaffold_1	phytozome6	CDS	74076	74235	.	+	0	Parent=POPTR_0001s00220.1;PACid=18237390
scaffold_1	phytozome6	CDS	74359	74634	.	+	2	Parent=POPTR_0001s00220.1;PACid=18237390
scaffold_1	phytozome6	CDS	75259	75893	.	+	2	Parent=POPTR_0001s00220.1;PACid=18237390
scaffold_1	phytozome6	gene	80191	81289	.	-	.	ID=POPTR_0001s00230;Name=POPTR_0001s00230
scaffold_1	phytozome6	mRNA	80191	81289	.	-	.	ID=POPTR_0001s00230.1;Name=POPTR_0001s00230.1;PACid=18235601;Parent=POPTR_0001s00230
scaffold_1	phytozome6	CDS	81161	81289	.	-	0	Parent=POPTR_0001s00230.1;PACid=18235601
scaffold_1	phytozome6	CDS	80191	80385	.	-	0	Parent=POPTR_0001s00230.1;PACid=18235601

I hope you can clearly see the issue now.Thank you

Last edited by shen; 02-21-2011 at 02:40 AM..
 

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