How to sort a text file if certain columns are blank?

Shell Programming and Scripting
1

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:

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:

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.

2

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

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 
	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

The one in red is column 2. The full rows, column 2 is blank. Sorry for the confusion.

6

Well, numerically empty is less than 1 (at least, as far as sort is concerned).

You could do:

sort -t$'\t' -k3 -n file.txt

But that will put empty ones last.

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

7

Dear CarloM,

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

Thanks.

8

What error/output do you get? What's your OS?

9

I'm guessing that the field separator may play a part here. Can you re-display your sample input using <sp> for a space and <tab> for tabs etc. so it's easy to see what we have as input. It might get quite into the geek mode, but we need to know the characters being sent, not what they look like on screen.

Regards,
Robin

10

Dear rbatte

I modify the input file and output file to make it easier to see. Both are tab-delimited files and blank columns are indicated by <Blank> . Basically, I have an original table containing 29 lines (the top 29 lines). I want to insert another 24 lines (the last 24 lines in the input file) of information in to the table. I want to sort according to column 2, 3, 4 but column 1 has to be in ascending order. Column 3 and 4 could be either ascending or descending. It is quite complicated.

Input:

1	A_scaffold000011	4339168	4339469	<Blank>
2	A_scaffold000011	4336216	4336952	<Blank>
3	A_scaffold000011	4335744	4336451	<Blank>
4	A_scaffold000011	4326850	4327454	<Blank>
5	A_scaffold000066	574913	575350	<Blank>
6	A_scaffold000011	4315302	4316020	<Blank>
7	A_scaffold000011	4312997	4313537	<Blank>
8	A_scaffold000011	4309058	4309666	<Blank>
9	A_scaffold000011	4303984	4304718	<Blank>
10	A_scaffold000011	4296794	4297091	<Blank>
11	A_scaffold000011	4296721	4297091	<Blank>
12	A_scaffold000011	4294183	4294527	<Blank>
13	A_scaffold000011	4293159	4294160	<Blank>
14	A_scaffold000011	4291440	4291890	<Blank>
15	A_scaffold000011	4289872	4290250	<Blank>
16	A_scaffold000011	4286640	4286947	<Blank>
17	A_scaffold000011	4286521	4286947	<Blank>
18	A_scaffold000011	4280797	4281196	<Blank>
19	A_scaffold000014	794245	794488	<Blank>
20	A_scaffold000014	794255	794488	<Blank>
21	A_scaffold000014	795894	796054	<Blank>
22	A_scaffold000014	808242	808642	<Blank>
23	A_scaffold000014	820613	820924	<Blank>
24	A_scaffold000014	829870	830251	<Blank>
25	A_scaffold000014	838447	838648	<Blank>
26	A_scaffold000014	838939	839062	<Blank>
27	A_scaffold000014	842685	842840	<Blank>
28	A_scaffold000014	843537	844392	<Blank>
29	A_scaffold000014	846997	847407	<Blank>
<Blank>	A_Scaffold000011	4364401	4364470	3129698
<Blank>	A_Scaffold000011	4358728	4358797	4168785
<Blank>	A_Scaffold000011	4323020	4323066	3139239
<Blank>	A_Scaffold000011	4235019	4235088	3163667
<Blank>	A_Scaffold000011	4223720	4223777	4118279
<Blank>	A_Scaffold000011	4223656	4223724	4331816
<Blank>	A_Scaffold000011	4082016	4082081	3118055
<Blank>	A_Scaffold000011	4023447	4023497	4332841
<Blank>	A_Scaffold000011	4023447	4023493	4116222
<Blank>	A_Scaffold000011	4021097	4021166	3091511
<Blank>	A_Scaffold000011	4011579	4011633	3087884
<Blank>	A_Scaffold000014	171832	171887	4335868
<Blank>	A_Scaffold000014	270626	270691	3087214
<Blank>	A_Scaffold000014	333155	333224	3117688
<Blank>	A_Scaffold000014	333219	333288	4111260
<Blank>	A_Scaffold000014	400018	400087	3122030
<Blank>	A_Scaffold000014	400195	400264	3150239
<Blank>	A_Scaffold000014	732332	732401	4167274
<Blank>	A_Scaffold000014	840515	840584	4119431
<Blank>	A_Scaffold000014	856967	857035	3131230
<Blank>	A_Scaffold000014	857030	857099	3146145
<Blank>	A_Scaffold000014	876175	876232	4169013
<Blank>	A_Scaffold000014	895598	895631	3217934
<Blank>	A_Scaffold000014	899441	899481	4112189

Output file:

<Blank>	A_Scaffold000011	4364401	4364470	3129698
<Blank>	A_Scaffold000011	4358728	4358797	4168785
1	A_scaffold000011	4339168	4339469	<Blank>
2	A_scaffold000011	4336216	4336952	<Blank>
3	A_scaffold000011	4335744	4336451	<Blank>
4	A_scaffold000011	4326850	4327454	<Blank>
<Blank>	A_Scaffold000011	4323020	4323066	3139239
5	A_scaffold000066	574913	575350	<Blank>
6	A_scaffold000011	4315302	4316020	<Blank>
7	A_scaffold000011	4312997	4313537	<Blank>
8	A_scaffold000011	4309058	4309666	<Blank>
9	A_scaffold000011	4303984	4304718	<Blank>
10	A_scaffold000011	4296794	4297091	<Blank>
11	A_scaffold000011	4296721	4297091	<Blank>
12	A_scaffold000011	4294183	4294527	<Blank>
13	A_scaffold000011	4293159	4294160	<Blank>
14	A_scaffold000011	4291440	4291890	<Blank>
15	A_scaffold000011	4289872	4290250	<Blank>
16	A_scaffold000011	4286640	4286947	<Blank>
17	A_scaffold000011	4286521	4286947	<Blank>
18	A_scaffold000011	4280797	4281196	<Blank>
<Blank>	A_Scaffold000011	4235019	4235088	3163667
<Blank>	A_Scaffold000011	4223720	4223777	4118279
<Blank>	A_Scaffold000011	4223656	4223724	4331816
<Blank>	A_Scaffold000011	4082016	4082081	3118055
<Blank>	A_Scaffold000011	4023447	4023497	4332841
<Blank>	A_Scaffold000011	4023447	4023493	4116222
<Blank>	A_Scaffold000011	4021097	4021166	3091511
<Blank>	A_Scaffold000011	4011579	4011633	3087884
<Blank>	A_Scaffold000014	171832	171887	4335868
<Blank>	A_Scaffold000014	270626	270691	3087214
<Blank>	A_Scaffold000014	333155	333224	3117688
<Blank>	A_Scaffold000014	333219	333288	4111260
<Blank>	A_Scaffold000014	400018	400087	3122030
<Blank>	A_Scaffold000014	400195	400264	3150239
<Blank>	A_Scaffold000014	732332	732401	4167274
19	A_scaffold000014	794245	794488	<Blank>
20	A_scaffold000014	794255	794488	<Blank>
21	A_scaffold000014	795894	796054	<Blank>
22	A_scaffold000014	808242	808642	<Blank>
23	A_scaffold000014	820613	820924	<Blank>
24	A_scaffold000014	829870	830251	<Blank>
25	A_scaffold000014	838447	838648	<Blank>
26	A_scaffold000014	838939	839062	<Blank>
<Blank>	A_Scaffold000014	840515	840584	4119431
27	A_scaffold000014	842685	842840	<Blank>
28	A_scaffold000014	843537	844392	<Blank>
29	A_scaffold000014	846997	847407	<Blank>
<Blank>	A_Scaffold000014	856967	857035	3131230
<Blank>	A_Scaffold000014	857030	857099	3146145
<Blank>	A_Scaffold000014	876175	876232	4169013
<Blank>	A_Scaffold000014	895598	895631	3217934
<Blank>	A_Scaffold000014	899441	899481	4112189
11

Well, I regret that is of little use. I asked you to replace the space and tab characters so we can see the file byte-by-byte. All the white-space and the <Blank> markers just confuse it.

It might make it messy, but perhaps you could run the following:-

tr " \t" "^~" < filename

It will convert the spaces to a carat ^ and the tabs to a tilde ~ so we can see what is what. Please do not alter the file in any other way to point out blank columns, but feel free to describe them or highlight them with a colour.

If we can read the input clearly, then we can work on helping you.

As an example:-

$ cat infile
Here is a line then a tab       tab bit

$ tr " \t" "^~" < infile
Here^is^a^line^then^a^tab~tab^bit

Regards,

Robin