gce-1.0.1.tar.gz

Author: galaxy001

Howto.txt

@@ -3,8 +3,8 @@ more information, you can read the published manuscript.
 
 1. How to finish a simple run?
 ./gce -f kmer_depth_file >gce.table 2>gce.log ##basic standard discrete model.
-./gce -f kmer_depth_file -c unique_depth -H 1 >gce.table 2>gce.log ##for heterozygous mode.
-./gce -f Kmer_depth_file -c unqiue_depth -m 1 -D 8 >gce.table 2> gce.log  ##for continuous model
+./gce -f kmer_depth_file -c kmer_num -H 1 >gce.table 2>gce.log ##for heterozygous mode.
+./gce -f Kmer_depth_file -c kmer_num -m 1 -D 8 >gce.table 2> gce.log  ##for continuous model
 
 2. How to get a proper genome size?
 Firstly, you need to set -g total_kmer_num. You can obtain the value from the output of kmer frequence count programs.
@@ -34,7 +34,7 @@ In the gce, we will estimate Kmer Heterozygous Ratio(KHR) based on the formula:
 To get the Base Heterozygous Ratio(BHR), you can use the formula: BHR = KHR/Kmer(suppose each snp cause K new kmers).
 
 5. How to decide whether use continuous model or discrete model?
-The performance of the two model is quite similar. For real sequencing data, continuous model is more suitable, however, its stability should be improved.
+The performance of the two model is quite similar. For real sequencing data, it is proper to use continuous model.
 
 6. How to treat the situation when the peak recognized is wrong?
 You just set -c , then the peak around the c value will be recognized. This is

README.txt

@@ -30,8 +30,8 @@ Options:
 	hybrid mode.
 -b	when there is sequencing bias, you need to set the value.
 
--m	estiation mode, there are standard discrete model(default) and continuous model. You can
-	set 1 to use continuous model, but its stability is not well.
+-m	estiation mode, there are standard discrete model(default) and continuous model, you can
+	set 1 to use continuous model.
 
 -D	set the raw distance for continuous model, which decide the peak
 	number.

Update.log

@@ -1,3 +1,10 @@
+
+version v1.0.1 Mar 18th 2012
+-------------------------------------------
+1. changed the output detail.
+2. fixed the input file format bugs.
+
+
 version v1.0.0  Dec 9th 2011
 -------------------------------------------
 This is the first published version.

gce

@@ -1,225 +1,57 @@
-#ai table:
-#i	c[i]	a[i]	C[i]	b[i]
-1	20.9675	0.915339	21.0312	0.796442
-2	41.9349	0.0607105	42.0623	0.104791
-3	62.9024	0.0117863	63.0935	0.0303871
-4	83.8699	0.00444268	84.1246	0.0157976
-5	104.837	0.00154009	105.156	0.00396374
-6	125.805	0.00451054	126.187	0.0486182
-#depth	real_P(x)	real_F(x)	est_P(x)	est_F(x)
-1	1.58085e-07	6.54959e-09	1.50419e-08	5.90122e-10
-2	5.33537e-07	4.42097e-08	1.57633e-07	1.2324e-08
-3	1.59073e-06	1.97716e-07	1.10163e-06	1.29494e-07
-4	8.28958e-06	1.37378e-06	5.77445e-06	9.07653e-07
-5	3.14984e-05	6.52503e-06	2.42149e-05	4.77201e-06
-6	0.000102222	2.54108e-05	8.46204e-05	2.00718e-05
-7	0.000299176	8.67657e-05	0.000253468	7.0355e-05
-8	0.000782995	0.000259521	0.000664321	0.000211377
-9	0.00178528	0.000665692	0.00154768	0.000555687
-10	0.00364236	0.00150906	0.00324509	0.00129853
-11	0.00677869	0.00308931	0.00618558	0.00273095
-12	0.0116204	0.0057773	0.010808	0.00522137
-13	0.0183176	0.00986585	0.0174321	0.00915098
-14	0.0269214	0.0156153	0.0261077	0.0148043
-15	0.0371294	0.0230745	0.0364943	0.0222396
-16	0.0480229	0.031834	0.0478249	0.0311819
-17	0.0585401	0.0412312	0.0589871	0.0409875
-18	0.067676	0.0504697	0.068713	0.050708
-19	0.0741762	0.0583904	0.0758309	0.0592493
-20	0.0775377	0.064249	0.0795038	0.0655875
-21	0.0774256	0.0673639	0.0793886	0.0689767
-22	0.0740053	0.0674542	0.0756762	0.0690922
-23	0.0676936	0.0645058	0.0690108	0.0660718
-24	0.0596138	0.0592764	0.0603262	0.0604524
-25	0.0504527	0.0522574	0.0506502	0.0530325
-26	0.0412656	0.0444514	0.0409288	0.0447037
-27	0.0325922	0.0364587	0.0319053	0.0362968
-28	0.0249678	0.0289642	0.0240652	0.0284735
-29	0.0186777	0.0224411	0.0176413	0.0216748
-30	0.0136385	0.0169517	0.0126586	0.0161215
-31	0.00988846	0.0127003	0.00899805	0.0118506
-32	0.00721296	0.00956284	0.00645989	0.00876938
-33	0.00542482	0.00741691	0.00481601	0.00670934
-34	0.00434923	0.00612654	0.00384554	0.00547208
-35	0.00373408	0.00541472	0.00335478	0.00486047
-36	0.00347158	0.0051779	0.00318489	0.0046967
-37	0.00340248	0.0052158	0.00321156	0.00482965
-38	0.00345468	0.00543895	0.00334078	0.00513568
-39	0.003526	0.00569731	0.00350335	0.00551602
-40	0.00361658	0.00599351	0.00364994	0.00589343
-41	0.0036418	0.0061862	0.00374714	0.00620941
-42	0.00362364	0.00630548	0.00377466	0.00642221
-43	0.00353197	0.0062923	0.00372329	0.00650573
-44	0.00338255	0.00616625	0.00359315	0.00644862
-45	0.0031635	0.00589798	0.00339198	0.00625309
-46	0.00291887	0.00556283	0.0031333	0.00593322
-47	0.00264164	0.00514393	0.00283432	0.00551248
-48	0.00236521	0.00470364	0.00251387	0.00502067
-49	0.00208134	0.00422534	0.00219037	0.00449051
-50	0.00180902	0.00374745	0.00188024	0.00395429
-51	0.00156358	0.0033038	0.00159658	0.00344095
-52	0.00135086	0.00291029	0.00134858	0.00297392
-53	0.00116761	0.00256387	0.00114133	0.00256975
-54	0.0010258	0.00229499	0.000976066	0.00223773
-55	0.000912772	0.00207993	0.000850877	0.00198029
-56	0.000824956	0.001914	0.000761442	0.00179399
-57	0.000758333	0.00179085	0.000701914	0.00167091
-58	0.000712311	0.00171167	0.000665719	0.00160013
-59	0.000687393	0.00168028	0.00064624	0.00156921
-60	0.000661299	0.00164389	0.000637333	0.00156547
-61	0.000647625	0.00163673	0.00063368	0.00157702
-62	0.000637053	0.0016364	0.000630996	0.00159347
-63	0.000617697	0.00161228	0.000626099	0.00160644
-64	0.00060015	0.00159134	0.00061689	0.00160971
-65	0.000577543	0.00155533	0.000602262	0.00159934
-66	0.000551914	0.00150917	0.000581961	0.00157347
-67	0.000526818	0.00146238	0.000556418	0.00153208
-68	0.000495705	0.00139655	0.000526573	0.00147671
-69	0.000464295	0.00132729	0.000493693	0.00141002
-70	0.000434664	0.0012606	0.000459207	0.00133544
-71	0.000404006	0.00118842	0.000424552	0.00125674
-72	0.000374977	0.00111856	0.000391052	0.00117769
-73	0.00035001	0.00105859	0.000359817	0.00110173
-74	0.000328668	0.00100766	0.000331684	0.00103173
-75	0.000304738	0.000946917	0.000307186	0.000969806
-76	0.000292279	0.000920312	0.000286549	0.000917274
-77	0.000270631	0.000863361	0.000269717	0.000874598
-78	0.000259368	0.000838175	0.000256395	0.000841476
-79	0.000250011	0.000818296	0.000246107	0.000816945
-80	0.000237592	0.00078749	0.000238256	0.000799541
-81	0.000233057	0.000782114	0.00023219	0.000787468
-82	0.000226407	0.00076918	0.000227257	0.000778782
-83	0.000222929	0.0007666	0.000222854	0.000771557
-84	0.000220341	0.000766827	0.000218466	0.000764027
-85	0.0002138	0.000752922	0.000213689	0.000754708
-86	0.000206795	0.000736821	0.000208244	0.00074247
-87	0.000201331	0.000725694	0.000201979	0.000726587
-88	0.000192617	0.000702263	0.000194857	0.000706746
-89	0.000184633	0.000680806	0.000186948	0.000683027
-90	0.000177628	0.000662335	0.000178401	0.000655858
-91	0.000175474	0.000661574	0.000169425	0.000625959
-92	0.000165821	0.00063205	0.000160263	0.000594263
-93	0.000158213	0.000609607	0.000151169	0.000561849
-94	0.000151366	0.000589496	0.000142391	0.000529863
-95	0.000148382	0.000584023	0.000134153	0.000499453
-96	0.000143294	0.000569932	0.000126642	0.000471716
-97	0.0001395	0.000560621	0.000120003	0.000447653
-98	0.000135024	0.000548228	0.000114334	0.000428143
-99	0.000128217	0.0005259	0.00010969	0.000413925
-100	0.000127446	0.00052802	0.000106086	0.000405597
-101	0.000124097	0.000519284	0.000103503	0.000403621
-102	0.000121389	0.000512985	0.000101894	0.000408334
-103	0.000117754	0.000502498	0.000101196	0.000419964
-104	0.000114533	0.000493498	0.000101335	0.000438645
-105	0.000113297	0.000492871	0.000102233	0.00046443
-106	0.000109296	0.000479992	0.000103813	0.000497302
-107	0.000107853	0.000478125	0.000106003	0.000537173
-108	0.000103486	0.000463053	0.000108736	0.000583884
-109	0.000102449	0.000462655	0.000111952	0.000637192
-110	0.000101896	0.000464378	0.000115595	0.000696765
-111	9.68369e-05	0.000445336	0.000119608	0.000762156
-112	9.2618e-05	0.000429771	0.000123935	0.000832794
-113	9.24303e-05	0.000432729	0.000128514	0.000907966
-114	8.80533e-05	0.000415886	0.000133277	0.000986806
-115	8.50892e-05	0.000405411	0.000138141	0.00106829
-116	8.29155e-05	0.00039849	0.000143018	0.00115123
-117	8.18682e-05	0.000396849	0.000147803	0.00123432
-118	7.88745e-05	0.000385605	0.000152384	0.0013161
-119	7.6602e-05	0.000377669	0.000156641	0.00139505
-120	7.44086e-05	0.000369937	0.000160448	0.00146956
-121	7.32526e-05	0.000367225	0.000163682	0.00153806
-122	7.03478e-05	0.000355577	0.000166221	0.001599
-123	6.9093e-05	0.000352097	0.000167957	0.00165092
-124	6.72157e-05	0.000345316	0.000168795	0.00169255
-125	6.43702e-05	0.000333364	0.00016866	0.00172278
-126	6.35798e-05	0.000331904	0.000167501	0.00174077
-127	6.1831e-05	0.000325337	0.000165291	0.00174596
-128	5.96079e-05	0.000316109	0.000162034	0.00173808
-129	5.88768e-05	0.000314671	0.000157759	0.0017172
-130	5.76318e-05	0.000310405	0.000152523	0.00168367
-131	5.78294e-05	0.000313866	0.000146406	0.00163817
-132	5.58237e-05	0.000305293	0.000139513	0.00158165
-133	5.55965e-05	0.000306353	0.000131962	0.00151527
-134	5.37588e-05	0.000298454	0.000123886	0.00144042
-135	5.1842e-05	0.000289961	0.000115426	0.00135862
-136	5.12492e-05	0.000288768	0.000106724	0.00127147
-137	4.92039e-05	0.000279283	9.79214e-05	0.00118061
-138	4.77021e-05	0.000272735	8.91513e-05	0.00108766
-139	4.74057e-05	0.000273004	8.05374e-05	0.000994167
-140	4.61114e-05	0.000267461	7.21894e-05	0.000901578
-141	4.65955e-05	0.000272199	6.42015e-05	0.000811186
-142	4.40859e-05	0.000259365	5.66504e-05	0.000724116
-143	4.37895e-05	0.000259436	4.95953e-05	0.000641304
-144	4.25644e-05	0.000253941	4.30776e-05	0.00056349
-145	4.05191e-05	0.000243418	3.71219e-05	0.000491217
-146	4.02919e-05	0.000243722	3.17376e-05	0.000424839
-147	3.95904e-05	0.000241119	2.69202e-05	0.000364534
-148	3.90075e-05	0.000239184	2.26538e-05	0.000310322
-149	3.82269e-05	0.000235982	1.8913e-05	0.000262089
-150	3.83751e-05	0.000238487	1.56652e-05	0.000219607
-151	3.68338e-05	0.000230434	1.28725e-05	0.000182559
-152	3.66065e-05	0.000230529	1.04941e-05	0.000150564
-153	3.52035e-05	0.000223152	8.4874e-06	0.000123196
-154	3.51344e-05	0.000224169	6.81015e-06	0.000100007
-155	3.3682e-05	0.000216298	5.42112e-06	8.05427e-05
-156	3.38005e-05	0.00021846	4.28125e-06	6.43546e-05
-157	3.38993e-05	0.000220503	3.3543e-06	5.10143e-05
-158	3.33164e-05	0.000218091	2.60724e-06	4.01202e-05
-159	3.24963e-05	0.00021407	2.01053e-06	3.13034e-05
-160	3.17158e-05	0.000210242	1.53811e-06	2.42315e-05
-161	3.01448e-05	0.000201077	1.16738e-06	1.86092e-05
-162	3.02831e-05	0.000203254	8.78997e-07	1.41785e-05
-163	2.94433e-05	0.000198837	6.56613e-07	1.07175e-05
-164	2.98286e-05	0.000202675	4.86609e-07	8.03742e-06
-165	2.87023e-05	0.000196211	3.57765e-07	5.97994e-06
-166	2.76846e-05	0.000190401	2.60954e-07	4.41403e-06
-167	2.76846e-05	0.000191548	1.88834e-07	3.23245e-06
-168	2.72795e-05	0.000189876	1.35563e-07	2.34848e-06
-169	2.73685e-05	0.000191629	9.65499e-08	1.69278e-06
-170	2.63804e-05	0.000185804	6.82197e-08	1.21052e-06
-171	2.57777e-05	0.000182627	4.78207e-08	8.58823e-07
-172	2.64693e-05	0.000188623	3.3256e-08	6.04494e-07
-173	2.47205e-05	0.000177185	2.29442e-08	4.22123e-07
-174	2.50565e-05	0.000180631	1.57044e-08	2.92445e-07
-175	2.49774e-05	0.000181096	1.0664e-08	2.01006e-07
-176	2.45822e-05	0.000179249	7.18398e-09	1.37066e-07
-177	2.40289e-05	0.00017621	4.8013e-09	9.27279e-08
-178	2.47106e-05	0.000182233	3.18346e-09	6.22371e-08
-179	2.38115e-05	0.000176589	2.09406e-09	4.14425e-08
-180	2.25963e-05	0.000168513	1.36655e-09	2.7378e-08
-181	2.28433e-05	0.000171301	8.84731e-10	1.79438e-08
-182	2.27247e-05	0.000171354	5.68256e-10	1.16677e-08
-183	2.25172e-05	0.000170722	3.62097e-10	7.52692e-09
-184	2.13316e-05	0.000162616	2.28904e-10	4.81732e-09
-185	2.14501e-05	0.000164409	1.43559e-10	3.05881e-09
-186	2.09463e-05	0.000161415	8.93211e-11	1.92689e-09
-187	2.03139e-05	0.000157383	5.51349e-11	1.20426e-09
-188	2.04226e-05	0.000159071	3.37634e-11	7.46695e-10
-189	1.97112e-05	0.000154347	2.05123e-11	4.59329e-10
-190	2.01855e-05	0.000158897	1.23632e-11	2.80325e-10
-191	1.82489e-05	0.000144409	7.39254e-12	1.6973e-10
-192	1.88022e-05	0.000149566	4.38536e-12	1.01956e-10
-193	1.89998e-05	0.000151925	2.58086e-12	6.07614e-11
-194	1.85453e-05	0.00014906	1.50686e-12	3.59252e-11
-195	1.90097e-05	0.00015358	8.72825e-13	2.10731e-11
-196	1.85552e-05	0.000150677	5.01569e-13	1.22636e-11
-197	1.81699e-05	0.0001483	2.85944e-13	7.08051e-12
-198	1.81402e-05	0.00014881	1.61726e-13	4.05574e-12
-199	1.80414e-05	0.000148747	9.07458e-14	2.3048e-12
-200	1.75178e-05	0.000145155	5.05151e-14	1.29944e-12
-201	1.79525e-05	0.000149501	2.78974e-14	7.26834e-13
-202	1.72807e-05	0.000144622	1.52846e-14	4.03342e-13
-203	1.70633e-05	0.00014351	8.30791e-15	2.2206e-13
-204	1.68459e-05	0.00014238	4.48e-15	1.2129e-13
-205	1.64902e-05	0.000140057	2.39669e-15	6.57262e-14
-206	1.62037e-05	0.000138295	1.27202e-15	3.53354e-14
-207	1.64606e-05	0.000141169	6.69766e-16	1.88469e-14
-208	1.65001e-05	0.000142192	3.49865e-16	9.97307e-15
-209	1.61839e-05	0.000140137	1.81312e-16	5.23571e-15
-210	1.62333e-05	0.000141238	9.32178e-17	2.72697e-15
-211	1.5601e-05	0.000136382	4.75467e-17	1.40911e-15
-212	1.5848e-05	0.000139198	2.40596e-17	7.22379e-16
-213	1.52256e-05	0.000134362	1.20783e-17	3.67405e-16
-214	1.45932e-05	0.000129386	6.01548e-18	1.85389e-16
-215	1.48205e-05	0.000132015	2.97223e-18	9.28069e-17
-216	1.45537e-05	0.000130242	1.45695e-18	4.6093e-17
+Load kmer depth frequency file...
+File load finished, the last depth is 255
+load node number 101211427 total kmer number 2442901555
+Possible peaks including: 20	41	
+Possible peaks including: 22	42	
+
+Raw kmer depth estiamtion:
+Curve	peak	expect_depth
+k-mer species 20	20.9696
+k-mer individuals 22	21.9947
+
+The estimate peak number is 6
+No valley, and may be no sequencing error!
+Initial ai...
+i	a[i]	c[i]
+1	0.872825	20.9696
+2	0.0591176	41.9393
+3	0.0126655	62.9089
+4	0.00511779	83.8786
+5	0.00293967	104.848
+6	0.00180986	125.818
+i	b[i]	C[i]
+1	0.776873	21.9947
+2	0.10461	43.9893
+3	0.0316688	65.984
+4	0.0170621	87.9787
+5	0.0121616	109.973
+6	0.00903791	131.968
+Initial ai and bi finished!
+start iterating using discrete model...
+C-iter number: 1	c distance: 1
+cvg is 20.9696 and node num is 101211427
+Cvg is 21.9947 and kmer num is 2442901555
+A-iter number: 1	distance: 1
+update now num: 101211427 now kmer: 2442901555
+A-iter number: 2	distance: 0.0080005
+update now num: 101211427 now kmer: 2442901555
+A-iter number: 3	distance: 0.000216786
+update now num: 101211427 now kmer: 2442901555
+Possible peaks including: 20	56	158	
+the unique peak is 20
+Possible peaks including: 22	61	84	102	169	
+the unique peak is 22
+C-iter number: 2	c distance: 0.000103993
+cvg is 20.9675 and node num is 101211427
+Cvg is 21.9887 and kmer num is 2442901555
+A-iter number: 1	distance: 1
+update now num: 101211427 now kmer: 2442901555
+Possible peaks including: 20	56	158	
+the unique peak is 20
+Possible peaks including: 22	61	84	103	169	
+the unique peak is 22
+
+Final estimation table:
+raw_peak	now_node	low_kmer	now_kmer	cvg	genome_size	a[1]	b[1]
+20	101211427	0	2442901555	20.9675	1.16509e+08	0.915339	0.799342
+Discrete mode estimation finished!