Using sed to find matched patterns and append

[BunnyMerah]

Hi,

I am a beginner and I would like to learn and explore sed as it is very powerful one liner to crunch huge data. I have thousands of data that I am working on. Below is the sample:-

chr1	OnePiece	Loc	01516	03251	.	-	.	g_id LINC01725 ;	t_id LINC01725:44 ;	g_alias_1 G233008 ;	g_alias_2 RP11-475O6.1 ;	g_alias_3 G233008.1 ;	g_alias_4 9930.1 ;	g_alias_5 G233008.5 ;	g_alias_6 LINC01725 ;	g_alias_7 LOC101927560 ;	t_alias_1 E457273 ;	t_alias_2 E457273.1 ;	t_alias_3 RP11-475O6.1-005 ;	t_alias_4 27496.1 ;	t_alias_5 NONHSAT004171 ;	t_alias_6 NR_119374 ;	t_alias_7 E457273.5 ;	t_alias_8 NR_119374.1 ;
chr1	OnePiece	Loc	49907	50022	.	-	.	g_id LINC01725 ;	t_id LINC01725:44 ;	g_alias_1 G233008 ;	g_alias_2 RP11-475O6.1 ;	g_alias_3 G233008.1 ;	g_alias_4 9930.1 ;	g_alias_5 G233008.5 ;	g_alias_6 LINC01725 ;	g_alias_7 LOC101927560 ;	t_alias_1 E457273 ;	t_alias_2 E457273.1 ;	t_alias_3 RP11-475O6.1-005 ;	t_alias_4 27496.1 ;	t_alias_5 NONHSAT004171 ;	t_alias_6 NR_119374 ;	t_alias_7 E457273.5 ;	t_alias_8 NR_119374.1 ;
chr1	OnePiece	Loc	60408	60546	.	-	.	g_id LINC01725 ;	t_id LINC01725:44 ;	g_alias_1 G233008 ;	g_alias_2 RP11-475O6.1 ;	g_alias_3 G233008.1 ;	g_alias_4 9930.1 ;	g_alias_5 G233008.5 ;	g_alias_6 LINC01725 ;	g_alias_7 LOC101927560 ;	t_alias_1 E457273 ;	t_alias_2 E457273.1 ;	t_alias_3 RP11-475O6.1-005 ;	t_alias_4 27496.1 ;	t_alias_5 NONHSAT004171 ;	t_alias_6 NR_119374 ;	t_alias_7 E457273.5 ;	t_alias_8 NR_119374.1 ;
chr16	OnePiece	Loc	92392	92726	.	-	.	g_id lnc-ZFHX3-27 ;	t_id lnc-ZFHX3-27:11 ;	g_alias_1 G249447 ;	g_alias_2 XLOC_012007 ;	g_alias_3 linc-ZFHX3-2 ;	g_alias_4 G261404.1 ;	g_alias_5 AC009120.4 ;	g_alias_6 176255.2 ;	g_alias_7 G261404.5 ;	g_alias_8 G261404.6 ;	g_alias_9 AC138627.1 ;	g_alias_10 LOC101928035 ;	t_alias_1 E510251 ;	t_alias_2 TCONS_00024274 ;	t_alias_3 E568137.1 ;	t_alias_4 AC009120.4-001 ;	t_alias_5 431686.1 ;	t_alias_6 NONHSAT143655 ;	t_alias_7 NR_104657 ;	t_alias_8 NR_104657.1 ;
chr16	OnePiece	Loc	05905	06165	.	-	.	g_id lnc-ZFHX3-27 ;	t_id lnc-ZFHX3-27:11 ;	g_alias_1 G249447 ;	g_alias_2 XLOC_012007 ;	g_alias_3 linc-ZFHX3-2 ;	g_alias_4 G261404.1 ;	g_alias_5 AC009120.4 ;	g_alias_6 176255.2 ;	g_alias_7 G261404.5 ;	g_alias_8 G261404.6 ;	g_alias_9 AC138627.1 ;	g_alias_10 LOC101928035 ;	t_alias_1 E510251 ;	t_alias_2 TCONS_00024274 ;	t_alias_3 E568137.1 ;	t_alias_4 AC009120.4-001 ;	t_alias_5 431686.1 ;	t_alias_6 NONHSAT143655 ;	t_alias_7 NR_104657 ;	t_alias_8 NR_104657.1 ;
chr16	OnePiece	Loc	10306	10505	.	-	.	g_id lnc-ZFHX3-27 ;	t_id lnc-ZFHX3-27:11 ;	g_alias_1 G249447 ;	g_alias_2 XLOC_012007 ;	g_alias_3 linc-ZFHX3-2 ;	g_alias_4 G261404.1 ;	g_alias_5 AC009120.4 ;	g_alias_6 176255.2 ;	g_alias_7 G261404.5 ;	g_alias_8 G261404.6 ;	g_alias_9 AC138627.1 ;	g_alias_10 LOC101928035 ;	t_alias_1 E510251 ;	t_alias_2 TCONS_00024274 ;	t_alias_3 E568137.1 ;	t_alias_4 AC009120.4-001 ;	t_alias_5 431686.1 ;	t_alias_6 NONHSAT143655 ;	t_alias_7 NR_104657 ;	t_alias_8 NR_104657.1 ;
chr16	OnePiece	Loc	15352	15521	.	-	.	g_id lnc-ZFHX3-27 ;	t_id lnc-ZFHX3-27:11 ;	g_alias_1 G249447 ;	g_alias_2 XLOC_012007 ;	g_alias_3 linc-ZFHX3-2 ;	g_alias_4 G261404.1 ;	g_alias_5 AC009120.4 ;	g_alias_6 176255.2 ;	g_alias_7 G261404.5 ;	g_alias_8 G261404.6 ;	g_alias_9 AC138627.1 ;	g_alias_10 LOC101928035 ;	t_alias_1 E510251 ;	t_alias_2 TCONS_00024274 ;	t_alias_3 E568137.1 ;	t_alias_4 AC009120.4-001 ;	t_alias_5 431686.1 ;	t_alias_6 NONHSAT143655 ;	t_alias_7 NR_104657 ;	t_alias_8 NR_104657.1 ;

I need to find pattern " ;" and append the effected columns with quote (") and get the output as follows:-

chr1	OnePiece	Loc	01516	03251	.	-	.	g_id “LINC01725”;	t_id "LINC01725:44";	g_alias_1 "G233008";	g_alias_2 "RP11-475O6.1";	g_alias_3 "G233008.1";	g_alias_4 "9930.1";	g_alias_5 "G233008.5";	g_alias_6 "LINC01725";	g_alias_7 "LOC101927560";	t_alias_1 "E457273";	t_alias_2 "E457273.1";	t_alias_3 "RP11-475O6.1-005";	t_alias_4 "27496.1";	t_alias_5 "NONHSAT004171";	t_alias_6 "NR_119374";	t_alias_7 "E457273.5";	t_alias_8 "NR_119374.1";
chr1	OnePiece	Loc	49907	50022	.	-	.	g_id "LINC01725";	t_id "LINC01725:44";	g_alias_1 "G233008";	g_alias_2 "RP11-475O6.1";	g_alias_3 "G233008.1";	g_alias_4 "9930.1";	g_alias_5 "G233008.5";	g_alias_6 "LINC01725";	g_alias_7 "LOC101927560";	t_alias_1 "E457273";	t_alias_2 "E457273.1";	t_alias_3 "RP11-475O6.1-005";	t_alias_4 "27496.1";	t_alias_5 "NONHSAT004171";	t_alias_6 "NR_119374";	t_alias_7 "E457273.5";	t_alias_8 "NR_119374.1";
chr1	OnePiece	Loc	60408	60546	.	-	.	g_id "LINC01725";	t_id "LINC01725:44";	g_alias_1 "G233008";	g_alias_2 "RP11-475O6.1";	g_alias_3 "G233008.1";	g_alias_4 "9930.1";	g_alias_5 "G233008.5";	g_alias_6 "LINC01725";	g_alias_7 "LOC101927560";	t_alias_1 "E457273";	t_alias_2 "E457273.1";	t_alias_3 "RP11-475O6.1-005";	t_alias_4 "27496.1";	t_alias_5 "NONHSAT004171";	t_alias_6 "NR_119374";	t_alias_7 "E457273.5";	t_alias_8 "NR_119374.1";
chr16	OnePiece	Loc	92392	92726	.	-	.	g_id "lnc-ZFHX3-27";	t_id "lnc-ZFHX3-27:11";	g_alias_1 "G249447";	g_alias_2 "XLOC_012007";	g_alias_3 "linc-ZFHX3-2";	g_alias_4 "G261404.1";	g_alias_5 "AC009120.4";	g_alias_6 "176255.2";	g_alias_7 "G261404.5";	g_alias_8 "G261404.6";	g_alias_9 "AC138627.1";	g_alias_10 "LOC101928035";	t_alias_1 "E510251";	t_alias_2 "TCONS_00024274";	t_alias_3 "E568137.1";	t_alias_4 "AC009120.4-001";	t_alias_5 "431686.1";	t_alias_6 "NONHSAT143655";	t_alias_7 "NR_104657";	t_alias_8 "NR_104657.1";
chr16	OnePiece	Loc	05905	06165	.	-	.	g_id "lnc-ZFHX3-27";	t_id "lnc-ZFHX3-27:11";	g_alias_1 "G249447";	g_alias_2 "XLOC_012007";	g_alias_3 "linc-ZFHX3-2";	g_alias_4 "G261404.1";	g_alias_5 "AC009120.4";	g_alias_6 "176255.2";	g_alias_7 "G261404.5";	g_alias_8 "G261404.6";	g_alias_9 "AC138627.1";	g_alias_10 "LOC101928035";	t_alias_1 "E510251";	t_alias_2 "TCONS_00024274";	t_alias_3 "E568137.1";	t_alias_4 "AC009120.4-001";	t_alias_5 "431686.1";	t_alias_6 "NONHSAT143655";	t_alias_7 "NR_104657";	t_alias_8 "NR_104657.1";
chr16	OnePiece	Loc	10306	10505	.	-	.	g_id "lnc-ZFHX3-27";	t_id "lnc-ZFHX3-27:11";	g_alias_1 "G249447";	g_alias_2 "XLOC_012007";	g_alias_3 "linc-ZFHX3-2";	g_alias_4 "G261404.1";	g_alias_5 "AC009120.4";	g_alias_6 "176255.2";	g_alias_7 "G261404.5";	g_alias_8 "G261404.6";	g_alias_9 "AC138627.1";	g_alias_10 "LOC101928035";	t_alias_1 "E510251";	t_alias_2 "TCONS_00024274";	t_alias_3 "E568137.1";	t_alias_4 "AC009120.4-001";	t_alias_5 "431686.1";	t_alias_6 "NONHSAT43655";	t_alias_7 "NR_104657";	t_alias_8 "NR_104657.1";
chr16	OnePiece	Loc	15352	15521	.	-	.	g_id "lnc-ZFHX3-27";	t_id "lnc-ZFHX3-27:11";	g_alias_1 "G249447";	g_alias_2 "XLOC_012007";	g_alias_3 "linc-ZFHX3-2";	g_alias_4 "G261404.1";	g_alias_5 "AC009120.4";	g_alias_6 "176255.2";	g_alias_7 "G261404.5";	g_alias_8 "G261404.6";	g_alias_9 "AC138627.1";	g_alias_10 "LOC101928035";	t_alias_1 "E510251";	t_alias_2 "TCONS_00024274";	t_alias_3 "E568137.1";	t_alias_4 "AC009120.4-001";	t_alias_5 "431686.1";	t_alias_6 "NONHSAT143655";	t_alias_7 "NR_104657";	t_alias_8 "NR_104657.1";

I tried playing around with the following codes and it almost worked.

sed 's/ /\"/g' inputfile

but couldn't get the output that I wanted as above, where there should be a blank space after the field id. For instance:-

The result should be g_id "lnc-ZFHX3-27"; NOT g_id"lnc-ZFHX3-27";

Just need a little bit more help here. thanks

 

[johnherman]

I suggest you post in one of these other forums, as your question is not AIX specific; you will get more people's eyes on it. One is for awk, which is a close relative to sed. The other is for General Unix Scripting.

https://www.tek-tips.com/threadminder.cfm?pid=271

https://www.tek-tips.com/threadminder.cfm?pid=822

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