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# 1  
Old 04-15-2014
How to sort a text file if certain columns are blank?
Dear all,

I am trying to sort a text file based on column 3, 10, 11 and 12. But certain column are blank for some lines. Column 3 has to be in ascending order after sorting.

Part of my input file is as follows:
Code:
CN727990		1	A01	4703	5083	73.28	-	A_scaffold000011	4365605	4365985	73.28	+
ES265498		2	A01	5336	5526	96.34	-	A_scaffold000011	4365162	4365352	96.34	+
JCVI_7716		3	A01	7142	8144	99.2	-	A_scaffold000011	4362544	4363546	99.2	+
JCVI_971		4	A01	8303	8532	97.39	-	A_scaffold000011	4362156	4362385	97.39	+
JCVI_21108		5	A01	9482	10049	97.54	-	A_scaffold000011	4360639	4361206	97.54	+
JCVI_33880		6	A01	10784	11527	100	+	A_scaffold000011	4359161	4359904	100	-
JCVI_9277		7	A01	19181	19676	92.54	-	A_scaffold000011	4351012	4351507	92.54	+
JCVI_2864		8	A01	21972	22312	97.95	+	A_scaffold000011	4348376	4348716	97.95	-
JCVI_36001		9	A01	22366	22814	87.97	+	A_scaffold000011	4347874	4348322	87.97	-
JCVI_37860		10	A01	30408	30598	92.15	+	A_scaffold000011	4340090	4340280	92.15	-
JCVI_11713		11	A01	31219	31520	89.8	-	A_scaffold000011	4339168	4339469	89.8	+
JCVI_13631		12	A01	33736	34472	97.97	-	A_scaffold000011	4336216	4336952	97.97	+
EV063032		13	A01	34237	34944	95.76	-	A_scaffold000011	4335744	4336451	95.76	+
JCVI_34462		14	A01	43234	43838	95.04	-	A_scaffold000011	4326850	4327454	95.04	+
JCVI_26779		15	A01	49116	49527	79.23	-	A_scaffold000066	574913	575350	77.73	-
JCVI_4409		16	A01	54668	55386	84.44	-	A_scaffold000011	4315302	4316020	84.44	+
JCVI_24992		17	A01	57151	57691	89.69	-	A_scaffold000011	4312997	4313537	90.61	+
JCVI_35198		18	A01	61022	61630	90.39	+	A_scaffold000011	4309058	4309666	90.39	-
JCVI_14925		19	A01	65970	66704	94.97	+	A_scaffold000011	4303984	4304718	94.97	-
JCVI_21195		20	A01	73597	73894	91	-	A_scaffold000011	4296794	4297091	91	+
JCVI_31294		21	A01	73597	73967	87.87	-	A_scaffold000011	4296721	4297091	87.87	+
EE410133		22	A01	76161	76505	99.71	-	A_scaffold000011	4294183	4294527	99.71	+
JCVI_4474		23	A01	76528	77529	94.61	-	A_scaffold000011	4293159	4294160	94.71	+
JCVI_14643		24	A01	78798	79248	99.34	-	A_scaffold000011	4291440	4291890	99.34	+
JCVI_27884		25	A01	80438	80816	94.74	-	A_scaffold000011	4289872	4290250	94.74	+
JCVI_31731		26	A01	83734	84048	96.84	-	A_scaffold000011	4286640	4286947	97.09	+
JCVI_31415		27	A01	83741	84167	90.11	-	A_scaffold000011	4286521	4286947	90.11	+
EE481053		28	A01	89492	89891	99.5	-	A_scaffold000011	4280797	4281196	99.5	+
EV115930		29	A01	95569	95986	89.79	+	A_scaffold000011	4274702	4275119	89.79	-
EV144874		30	A01	106531	106823	100	-	A_scaffold000011	4263865	4264157	100	+
JCVI_41170		31	A01	114724	114959	84.02	+	A_scaffold000011	4255729	4255964	84.02	-
EE465280		32	A01	115840	116016	97.19	+	A_scaffold000011	4254672	4254848	97.19	-
JCVI_17454		33	A01	119295	119820	94.11	+	A_scaffold000011	4250868	4251393	94.11	-
JCVI_41499		34	A01	120322	120660	94.71	-	A_scaffold000011	4250028	4250366	94.71	+
JCVI_25374		35	A01	120408	120988	95.04	-	A_scaffold000011	4249700	4250280	95.04	+
EV075546		36	A01	122759	123331	79.62	+	A_scaffold000011	4247357	4247929	79.62	-
CV432070		37	A01	125009	125379	88.17	-	A_scaffold000011	4245309	4245679	88.17	+
JCVI_22378		38	A01	126295	127012	93.08	-	A_scaffold000011	4243676	4244393	93.08	+
JCVI_41232		39	A01	127446	128187	69.62	-	A_scaffold000011	4242501	4243242	75.07	+
JCVI_32947		40	A01	130071	130458	86.73	-	A_scaffold000011	4240230	4240617	86.73	+
JCVI_28932		41	A01	131558	132604	86.42	-	A_scaffold000011	4238084	4238728	98.3	+
JCVI_1030		42	A01	135456	135622	100	-	A_scaffold000011	4235066	4235232	100	+
JCVI_1606		43	A01	141142	141637	68.97	-	A_scaffold000011	4229051	4229546	68.77	+
JCVI_22632		44	A01	141698	142073	100	-	A_scaffold000011	4228615	4228990	100	+
JCVI_21754		45	A01	142505	142754	89.29	+	A_scaffold000011	4227934	4228183	89.29	-
JCVI_28714		46	A01	143816	144142	86.27	+	A_scaffold000011	4226546	4226872	86.27	-
EV159792		47	A01	151852	152208	95.8	+	A_scaffold000011	4218480	4218836	95.8	-
JCVI_33490		48	A01	153871	154537	91.49	+	A_scaffold000011	4216151	4216817	91.49	-
CV432635		49	A01	154030	154495	78.39	+	A_scaffold000011	4216193	4216658	78.39	-
ES990457		50	A01	154621	154967	89.97	+	A_scaffold000011	4215721	4216067	89.97	-
JCVI_15734		51	A01	160123	160689	75.17	+	A_scaffold000011	4209999	4210565	75.17	-
EE534878		52	A01	160424	160786	84.82	+	A_scaffold000011	4209902	4210264	84.82	-
EV044511		53	A01	160745	161164	100	+	A_scaffold000011	4209524	4209943	100	-
EE536766		54	A01	163447	163639	95.9	+	A_scaffold000011	4207049	4207241	95.9	-
CD836978		55	A01	163683	163843	97.52	+	A_scaffold000011	4206845	4207005	97.52	-
JCVI_26808		56	A01	164382	165055	89.19	+	A_scaffold000011	4205633	4206306	88.44	-
CD825163		57	A01	172600	173218	86.74	+	A_scaffold000011	4197470	4198088	86.58	-
JCVI_24875		58	A01	172778	174208	94.21	+	A_scaffold000011	4196480	4197910	94.14	-
EV018157		59	A01	192009	192640	99.53	+	A_scaffold000011	4178048	4178679	99.53	-
JCVI_36789		60	A01	203161	203895	98.5	+	A_scaffold000011	4166793	4167527	98.5	-
JCVI_34701		61	A01	205470	206494	98.63	+	A_scaffold000011	4164194	4165218	98.63	-
JCVI_40341		62	A01	205611	206110	98.2	+	A_scaffold000011	4164578	4165077	98.2	-
JCVI_32691		63	A01	208135	208994	95.25	-	A_scaffold000011	4161694	4162553	95.25	+
JCVI_817		64	A01	209558	209831	100	-	A_scaffold000011	4160857	4161130	100	+
JCVI_8832		65	A01	210559	210912	88.76	-	A_scaffold000011	4159776	4160129	88.76	+
EE565735		66	A01	213046	213450	98.02	+	A_scaffold000011	4157238	4157642	83.7	-
JCVI_39256		67	A01	213766	214035	91.27	+	A_scaffold000011	4156653	4156922	91.27	-
JCVI_40762		68	A01	213766	214163	96.25	+	A_scaffold000011	4156525	4156922	96.25	-
JCVI_23442		69	A01	216251	216849	99.5	-	A_scaffold000011	4153839	4154437	99.5	+
JCVI_18036		70	A01	217250	218021	91.34	-	A_scaffold000011	4152667	4153438	91.34	+
EX055842		71	A01	218103	218540	100	-	A_scaffold000011	4152148	4152585	100	+
JCVI_24203		72	A01	219341	220784	92.12	-	A_scaffold000011	4149904	4151347	92.12	+
EV084731		73	A01	224874	225346	91.08	+	A_scaffold000011	4145342	4145814	91.08	-
EE521944		74	A01	236246	236487	96.72	+	A_scaffold000011	4134201	4134442	96.72	-
EV080484		75	A01	237857	238154	97.99	+	A_scaffold000011	4132534	4132831	97.99	-
AM062389		76	A01	243555	244042	81.05	+	A_scaffold000011	4126646	4127133	81.05	-
JCVI_13543		77	A01	243573	245140	92.01	+	A_scaffold000011	4125548	4127115	92.01	-
DY001985		78	A01	246432	246698	98.13	+	A_scaffold000011	4128788	4129054	98.13	-
CX192439		79	A01	251278	251739	95.45	+	A_scaffold000011	4118949	4119410	95.45	-
ES984885		80	A01	253806	254088	81.66	+	A_scaffold000011	4116600	4116882	81.66	-
JCVI_19920		81	A01	257276	257927	87.76	+	A_scaffold000011	4112761	4113412	87.76	-
JCVI_21058		82	A01	258744	259084	97.65	+	A_scaffold000011	4111604	4111944	97.65	-
	3129698							A_Scaffold000011	4364401	4364470		
	4168785							A_Scaffold000011	4358728	4358797		
	3139239							A_Scaffold000011	4323020	4323066		
	3163667							A_Scaffold000011	4235019	4235088		
	4118279							A_Scaffold000011	4223720	4223777		
	4331816							A_Scaffold000011	4223656	4223724		
	3118055							A_Scaffold000011	4082016	4082081		
	4332841							A_Scaffold000011	4023447	4023497		
	4116222							A_Scaffold000011	4023447	4023493		
	3091511							A_Scaffold000011	4021097	4021166		
	3087884							A_Scaffold000011	4011579	4011633		
	4112653							A_Scaffold000011	3941727	3941791		
	4334276							A_Scaffold000011	3936334	3936368		
	3078010							A_Scaffold000011	3900432	3900498		
	3091117							A_Scaffold000011	3894770	3894834		
	3111703							A_Scaffold000011	3772414	3772469		
	4113921							A_Scaffold000011	3729680	3729749		
	3154078							A_Scaffold000011	3723694	3723748		
	4112922							A_Scaffold000011	3667296	3667365		
	3090679							A_Scaffold000011	3612608	3612677		
	3100582							A_Scaffold000011	3596445	3596487		
	3145603							A_Scaffold000011	3592682	3592734		
	4165519							A_Scaffold000011	3556093	3556161		
	3089388							A_Scaffold000011	3551924	3551993		
	4332850							A_Scaffold000011	3470849	3470900		
	3091818							A_Scaffold000011	3437105	3437174		
	4335561							A_Scaffold000011	3432071	3432138


I want the output as follows:
Code:
CN727990		1	A01	4703	5083	73.28	-	A_scaffold000011	4365605	4365985	73.28	+
ES265498		2	A01	5336	5526	96.34	-	A_scaffold000011	4365162	4365352	96.34	+
	3129698							A_Scaffold000011	4364401	4364470		
JCVI_7716		3	A01	7142	8144	99.2	-	A_scaffold000011	4362544	4363546	99.2	+
JCVI_971		4	A01	8303	8532	97.39	-	A_scaffold000011	4362156	4362385	97.39	+
JCVI_21108		5	A01	9482	10049	97.54	-	A_scaffold000011	4360639	4361206	97.54	+
JCVI_33880		6	A01	10784	11527	100	+	A_scaffold000011	4359161	4359904	100	-
	4168785							A_Scaffold000011	4358728	4358797		
JCVI_9277		7	A01	19181	19676	92.54	-	A_scaffold000011	4351012	4351507	92.54	+
JCVI_2864		8	A01	21972	22312	97.95	+	A_scaffold000011	4348376	4348716	97.95	-
JCVI_36001		9	A01	22366	22814	87.97	+	A_scaffold000011	4347874	4348322	87.97	-
JCVI_37860		10	A01	30408	30598	92.15	+	A_scaffold000011	4340090	4340280	92.15	-
JCVI_11713		11	A01	31219	31520	89.8	-	A_scaffold000011	4339168	4339469	89.8	+
JCVI_13631		12	A01	33736	34472	97.97	-	A_scaffold000011	4336216	4336952	97.97	+
EV063032		13	A01	34237	34944	95.76	-	A_scaffold000011	4335744	4336451	95.76	+
JCVI_34462		14	A01	43234	43838	95.04	-	A_scaffold000011	4326850	4327454	95.04	+
	3139239							A_Scaffold000011	4323020	4323066		
JCVI_26779		15	A01	49116	49527	79.23	-	A_scaffold000066	574913	575350	77.73	-
JCVI_4409		16	A01	54668	55386	84.44	-	A_scaffold000011	4315302	4316020	84.44	+
JCVI_24992		17	A01	57151	57691	89.69	-	A_scaffold000011	4312997	4313537	90.61	+
JCVI_35198		18	A01	61022	61630	90.39	+	A_scaffold000011	4309058	4309666	90.39	-
JCVI_14925		19	A01	65970	66704	94.97	+	A_scaffold000011	4303984	4304718	94.97	-
JCVI_21195		20	A01	73597	73894	91	-	A_scaffold000011	4296794	4297091	91	+
JCVI_31294		21	A01	73597	73967	87.87	-	A_scaffold000011	4296721	4297091	87.87	+
EE410133		22	A01	76161	76505	99.71	-	A_scaffold000011	4294183	4294527	99.71	+
JCVI_4474		23	A01	76528	77529	94.61	-	A_scaffold000011	4293159	4294160	94.71	+
JCVI_14643		24	A01	78798	79248	99.34	-	A_scaffold000011	4291440	4291890	99.34	+
JCVI_27884		25	A01	80438	80816	94.74	-	A_scaffold000011	4289872	4290250	94.74	+
JCVI_31731		26	A01	83734	84048	96.84	-	A_scaffold000011	4286640	4286947	97.09	+
JCVI_31415		27	A01	83741	84167	90.11	-	A_scaffold000011	4286521	4286947	90.11	+
EE481053		28	A01	89492	89891	99.5	-	A_scaffold000011	4280797	4281196	99.5	+
EV115930		29	A01	95569	95986	89.79	+	A_scaffold000011	4274702	4275119	89.79	-
EV144874		30	A01	106531	106823	100	-	A_scaffold000011	4263865	4264157	100	+
JCVI_41170		31	A01	114724	114959	84.02	+	A_scaffold000011	4255729	4255964	84.02	-
EE465280		32	A01	115840	116016	97.19	+	A_scaffold000011	4254672	4254848	97.19	-
JCVI_17454		33	A01	119295	119820	94.11	+	A_scaffold000011	4250868	4251393	94.11	-
JCVI_41499		34	A01	120322	120660	94.71	-	A_scaffold000011	4250028	4250366	94.71	+
JCVI_25374		35	A01	120408	120988	95.04	-	A_scaffold000011	4249700	4250280	95.04	+
EV075546		36	A01	122759	123331	79.62	+	A_scaffold000011	4247357	4247929	79.62	-
CV432070		37	A01	125009	125379	88.17	-	A_scaffold000011	4245309	4245679	88.17	+
JCVI_22378		38	A01	126295	127012	93.08	-	A_scaffold000011	4243676	4244393	93.08	+
JCVI_41232		39	A01	127446	128187	69.62	-	A_scaffold000011	4242501	4243242	75.07	+
JCVI_32947		40	A01	130071	130458	86.73	-	A_scaffold000011	4240230	4240617	86.73	+
JCVI_28932		41	A01	131558	132604	86.42	-	A_scaffold000011	4238084	4238728	98.3	+
JCVI_1030		42	A01	135456	135622	100	-	A_scaffold000011	4235066	4235232	100	+
	3163667							A_Scaffold000011	4235019	4235088		
JCVI_1606		43	A01	141142	141637	68.97	-	A_scaffold000011	4229051	4229546	68.77	+
JCVI_22632		44	A01	141698	142073	100	-	A_scaffold000011	4228615	4228990	100	+
JCVI_21754		45	A01	142505	142754	89.29	+	A_scaffold000011	4227934	4228183	89.29	-
JCVI_28714		46	A01	143816	144142	86.27	+	A_scaffold000011	4226546	4226872	86.27	-
	4118279							A_Scaffold000011	4223720	4223777		
	4331816							A_Scaffold000011	4223656	4223724		
EV159792		47	A01	151852	152208	95.8	+	A_scaffold000011	4218480	4218836	95.8	-
CV432635		49	A01	154030	154495	78.39	+	A_scaffold000011	4216193	4216658	78.39	-
JCVI_33490		48	A01	153871	154537	91.49	+	A_scaffold000011	4216151	4216817	91.49	-
ES990457		50	A01	154621	154967	89.97	+	A_scaffold000011	4215721	4216067	89.97	-
JCVI_15734		51	A01	160123	160689	75.17	+	A_scaffold000011	4209999	4210565	75.17	-
EE534878		52	A01	160424	160786	84.82	+	A_scaffold000011	4209902	4210264	84.82	-
EV044511		53	A01	160745	161164	100	+	A_scaffold000011	4209524	4209943	100	-
EE536766		54	A01	163447	163639	95.9	+	A_scaffold000011	4207049	4207241	95.9	-
CD836978		55	A01	163683	163843	97.52	+	A_scaffold000011	4206845	4207005	97.52	-
JCVI_26808		56	A01	164382	165055	89.19	+	A_scaffold000011	4205633	4206306	88.44	-
CD825163		57	A01	172600	173218	86.74	+	A_scaffold000011	4197470	4198088	86.58	-
JCVI_24875		58	A01	172778	174208	94.21	+	A_scaffold000011	4196480	4197910	94.14	-
EV018157		59	A01	192009	192640	99.53	+	A_scaffold000011	4178048	4178679	99.53	-
JCVI_36789		60	A01	203161	203895	98.5	+	A_scaffold000011	4166793	4167527	98.5	-
JCVI_40341		62	A01	205611	206110	98.2	+	A_scaffold000011	4164578	4165077	98.2	-
JCVI_34701		61	A01	205470	206494	98.63	+	A_scaffold000011	4164194	4165218	98.63	-
JCVI_32691		63	A01	208135	208994	95.25	-	A_scaffold000011	4161694	4162553	95.25	+
JCVI_817		64	A01	209558	209831	100	-	A_scaffold000011	4160857	4161130	100	+
JCVI_8832		65	A01	210559	210912	88.76	-	A_scaffold000011	4159776	4160129	88.76	+
EE565735		66	A01	213046	213450	98.02	+	A_scaffold000011	4157238	4157642	83.7	-
JCVI_39256		67	A01	213766	214035	91.27	+	A_scaffold000011	4156653	4156922	91.27	-
JCVI_40762		68	A01	213766	214163	96.25	+	A_scaffold000011	4156525	4156922	96.25	-
JCVI_23442		69	A01	216251	216849	99.5	-	A_scaffold000011	4153839	4154437	99.5	+
JCVI_18036		70	A01	217250	218021	91.34	-	A_scaffold000011	4152667	4153438	91.34	+
EX055842		71	A01	218103	218540	100	-	A_scaffold000011	4152148	4152585	100	+
JCVI_24203		72	A01	219341	220784	92.12	-	A_scaffold000011	4149904	4151347	92.12	+
EV084731		73	A01	224874	225346	91.08	+	A_scaffold000011	4145342	4145814	91.08	-
EE521944		74	A01	236246	236487	96.72	+	A_scaffold000011	4134201	4134442	96.72	-
EV080484		75	A01	237857	238154	97.99	+	A_scaffold000011	4132534	4132831	97.99	-
DY001985		78	A01	246432	246698	98.13	+	A_scaffold000011	4128788	4129054	98.13	-
AM062389		76	A01	243555	244042	81.05	+	A_scaffold000011	4126646	4127133	81.05	-
JCVI_13543		77	A01	243573	245140	92.01	+	A_scaffold000011	4125548	4127115	92.01	-
CX192439		79	A01	251278	251739	95.45	+	A_scaffold000011	4118949	4119410	95.45	-
ES984885		80	A01	253806	254088	81.66	+	A_scaffold000011	4116600	4116882	81.66	-
JCVI_19920		81	A01	257276	257927	87.76	+	A_scaffold000011	4112761	4113412	87.76	-
JCVI_21058		82	A01	258744	259084	97.65	+	A_scaffold000011	4111604	4111944	97.65	-
	3118055							A_Scaffold000011	4082016	4082081		
	4332841							A_Scaffold000011	4023447	4023497		
	4116222							A_Scaffold000011	4023447	4023493		
	3091511							A_Scaffold000011	4021097	4021166		
	3087884							A_Scaffold000011	4011579	4011633		
	4112653							A_Scaffold000011	3941727	3941791		
	4334276							A_Scaffold000011	3936334	3936368		
	3078010							A_Scaffold000011	3900432	3900498		
	3091117							A_Scaffold000011	3894770	3894834		
	3111703							A_Scaffold000011	3772414	3772469		
	4113921							A_Scaffold000011	3729680	3729749		
	3154078							A_Scaffold000011	3723694	3723748		
	4112922							A_Scaffold000011	3667296	3667365		
	3090679							A_Scaffold000011	3612608	3612677		
	3100582							A_Scaffold000011	3596445	3596487		
	3145603							A_Scaffold000011	3592682	3592734		
	4165519							A_Scaffold000011	3556093	3556161		
	3089388							A_Scaffold000011	3551924	3551993		
	4332850							A_Scaffold000011	3470849	3470900		
	3091818							A_Scaffold000011	3437105	3437174		
	4335561							A_Scaffold000011	3432071	3432138

How can I do by sort?

Thanks in advance.
Last edited by huiyee1; 04-15-2014 at 08:38 AM..
# 2  
Old 04-15-2014
It looks like full rows have 2 tabs between fields 1 and 2, but rows with missing data have only 1 tab before what appears to be field 2.

Is that the case, or is it just a formatting artifact and the file is really (single) tab-delimited?
# 3  
Old 04-15-2014
Quote:
Originally Posted by CarloM
It looks like full rows have 2 tabs between fields 1 and 2, but rows with missing data have only 1 tab before what appears to be field 2.

Is that the case, or is it just a formatting artifact and the file is really (single) tab-delimited?
Dear CarloM,

For some rows, column 2 is blank. For some some rows, column 1, 3, 4, 5, 6, 7, 8, 12, 13 are blank.
# 4  
Old 04-15-2014
Code:
	3129698							A_Scaffold000011	4364401	4364470

What column is this? Because if it's tab-delimited, that's column 2. If it's not column 2, what exactly is the format of your file?

EDIT: Ah, okay - so for the full(er) rows, column 2 is blank?
# 5  
Old 04-15-2014
Quote:
Originally Posted by CarloM
Code:
	3129698							A_Scaffold000011	4364401	4364470

What column is this? Because if it's tab-delimited, that's column 2. If it's not column 2, what exactly is the format of your file?

EDIT: Ah, okay - so for the full(er) rows, column 2 is blank?
The one in red is column 2. The full rows, column 2 is blank. Sorry for the confusion.
Last edited by huiyee1; 04-15-2014 at 08:55 AM..
# 6  
Old 04-15-2014
Well, numerically empty is less than 1 (at least, as far as sort is concerned).

You could do:
Code:
sort -t$'\t' -k3 -n file.txt

But that will put empty ones last.

EDIT: First, even (tired, sorry...)
# 7  
Old 04-15-2014
Quote:
Originally Posted by CarloM
Well, numerically empty is less than 1 (at least, as far as sort is concerned).

You could do:
Code:
sort -t$'\t' -k3 -n file.txt

But that will put empty ones last.

EDIT: First, even (tired, sorry...)
Dear CarloM,

It does not work. But, I appreciate your help.

Thanks.
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