Separated data from code by putting all data into data/ folder.

computePred.R

@@ -12,7 +12,7 @@ source(paste(Sys.getenv("ESGEMME_PATH"),"/pred.R",sep=""))
 aa = c("a","c","d","e","f","g","h","i","k","l","m","n","p","q","r","s","t","v","w","y")
 
 # BLOSUM62  matrix
-blosum62p = as.matrix(read.table(paste0(Sys.getenv("ESGEMME_PATH"),"/blosum62p.txt"),row.names=1))
+blosum62p = as.matrix(read.table(paste0(Sys.getenv("ESGEMME_PATH"),"/data/blosum62p.txt"),row.names=1))
 bgp = blosum62p[order(rownames(blosum62p)),order(colnames(blosum62p))]
 bg = apply(bgp,1,sum)
 

data/BLAT_jet.res

+AA	pos	chain	axs	cv	pc	tr	freq	trace	clusters	clusnumber	ssjetormax
+MET	1	A	1.0	0.1798	0.6606	0.0	0.0	0.0	0.0	0.0	0.0
+SER	2	A	1.0	0.4007	0.3574	0.0	0.0	0.0	0.0	0.0	0.0
+ILE	3	A	1.0	0.4642	0.638	0.0	0.0	0.0	0.0	0.0	0.0
+GLN	4	A	1.0	0.5616	0.4343	0.0971	0.18	0.0174	0.0	0.0	0.0174
+HIS	5	A	1.0	0.6781	0.5972	0.1113	0.06	0.0066	0.0	0.0	0.0066
+PHE	6	A	1.0	0.645	1.0	0.0928	0.12	0.0111	0.0	0.0	0.0111
+ARG	7	A	1.0	0.6488	0.5067	0.1249	0.34	0.0424	0.0	0.0	0.0424
+VAL	8	A	1.0	0.7859	0.5656	0.1094	0.54	0.059	0.0	0.0	0.059
+ALA	9	A	1.0	0.8354	0.3846	0.1142	0.52	0.0594	0.0	0.0	0.0594
+LEU	10	A	1.0	0.7349	0.7058	0.1591	0.14	0.0222	0.0	0.0	0.0222
+ILE	11	A	1.0	0.7358	0.638	0.1536	0.4	0.0614	0.0	0.0	0.0614
+PRO	12	A	1.0	0.7525	0.466	0.1143	0.38	0.0434	0.0	0.0	0.0434
+PHE	13	A	1.0	0.7142	1.0	0.1342	0.78	0.1047	0.0	0.0	0.1047
+PHE	14	A	1.0	0.686	1.0	0.1743	0.3	0.0522	0.0	0.0	0.0522
+ALA	15	A	1.0	0.8723	0.3846	0.21	0.7	0.147	0.0	0.0	0.147
+ALA	16	A	1.0	0.8165	0.3846	0.3606	0.34	0.1226	0.0	0.0	0.1226
+PHE	17	A	1.0	0.7198	1.0	0.2187	0.76	0.1662	0.0	0.0	0.1662
+CYS	18	A	1.0	0.7581	0.6425	0.2452	0.7	0.1716	0.0	0.0	0.1716
+LEU	19	A	1.0	0.7318	0.7058	0.2104	0.94	0.1978	0.0	0.0	0.1978
+PRO	20	A	1.0	0.6357	0.466	0.2601	0.74	0.1925	0.0	0.0	0.1925
+VAL	21	A	1.0	0.6017	0.5656	0.2712	0.54	0.1464	0.0	0.0	0.1464
+PHE	22	A	1.0	0.491	1.0	0.2798	0.52	0.1455	0.0	0.0	0.1455
+ALA	23	A	1.0	0.4599	0.3846	0.3037	0.92	0.2794	0.0	0.0	0.2794
+HIS	24	A	1.0	0.4471	0.5972	0.2954	0.68	0.2009	0.0	0.0	0.2009
+PRO	25	A	1.0	0.4918	0.466	0.2696	0.9	0.2426	0.0	0.0	0.2426
+GLU	26	A	1.0	0.4252	0.3348	0.3842	0.66	0.2536	0.0	0.0	0.38
+THR	27	A	1.0	0.5993	0.3257	0.5596	1.0	0.5596	0.0	0.0	0.5794
+LEU	28	A	1.0	0.5513	0.7058	0.3062	0.86	0.2633	0.0	0.0	0.6285
+VAL	29	A	1.0	0.443	0.5656	0.2447	0.82	0.2006	0.0	0.0	0.5043
+LYS	30	A	1.0	0.5102	0.2488	0.3921	0.9	0.3528	0.0	0.0	0.4315
+VAL	31	A	0.5	0.6384	0.5656	0.6009	0.98	0.5889	0.0	0.0	0.6136
+LYS	32	A	1.0	0.4541	0.2488	0.4482	0.88	0.3944	0.0	0.0	0.4242
+ASP	33	A	1.0	0.4253	0.3212	0.4874	0.72	0.3509	0.0	0.0	0.3881
+ALA	34	A	0.8	0.5623	0.3846	0.6821	1.0	0.6821	0.0	0.0	0.6222
+GLU	35	A	1.0	0.4961	0.3348	0.7952	1.0	0.7952	0.0	0.0	0.6457
+ASP	36	A	1.0	0.3478	0.3212	0.3964	0.82	0.325	0.0	0.0	0.3364
+GLN	37	A	1.0	0.357	0.4343	0.3527	0.92	0.3244	0.0	0.0	0.3956
+LEU	38	A	0.8	0.5159	0.7058	0.5341	1.0	0.5341	0.0	0.0	0.62
+GLY	39	A	1.0	0.3705	0.4117	0.6772	0.94	0.6365	0.0	0.0	0.5241
+ALA	40	A	1.0	0.489	0.3846	0.8016	1.0	0.8016	0.0	0.0	0.6453
+ARG	41	A	1.0	0.5109	0.5067	0.7641	1.0	0.7641	0.0	0.0	0.6375
+VAL	42	A	0.8	0.6763	0.5656	0.7475	1.0	0.7475	0.0	0.0	0.7119
+GLY	43	A	0.5	0.7337	0.4117	0.8915	1.0	0.8915	0.0	0.0	0.8126
+TYR	44	A	0.5	0.7363	0.7963	0.7625	1.0	0.7625	0.0	0.0	0.7794
+ILE	45	A	0.8	0.7024	0.638	0.557	0.98	0.5459	0.0	0.0	0.6702
+GLU	46	A	1.0	0.6608	0.3348	0.6645	1.0	0.6645	0.0	0.0	0.6626
+LEU	47	A	0.8	0.6131	0.7058	0.5707	1.0	0.5707	0.0	0.0	0.6594
+ASP	48	A	1.0	0.4773	0.3212	0.6963	1.0	0.6963	0.0	0.0	0.5868
+LEU	49	A	1.0	0.5763	0.7058	0.6209	1.0	0.6209	0.0	0.0	0.6634
+ASN	50	A	1.0	0.3649	0.3936	0.4828	0.96	0.4635	0.0	0.0	0.4286
+SER	51	A	1.0	0.3455	0.3574	0.4897	0.96	0.4702	0.0	0.0	0.4138
+GLY	52	A	1.0	0.4463	0.4117	0.7399	0.98	0.7251	0.0	0.0	0.5857
+LYS	53	A	1.0	0.3604	0.2488	0.3841	0.94	0.3611	0.0	0.0	0.3608
+ILE	54	A	1.0	0.4851	0.638	0.3776	0.92	0.3473	0.0	0.0	0.5616
+LEU	55	A	1.0	0.4936	0.7058	0.4812	0.98	0.4716	0.0	0.0	0.5997
+GLU	56	A	1.0	0.558	0.3348	0.2356	0.54	0.1272	0.0	0.0	0.4464
+SER	57	A	1.0	0.5527	0.3574	0.4512	0.86	0.388	0.0	0.0	0.4704
+PHE	58	A	1.0	0.5465	1.0	0.4883	1.0	0.4883	0.0	0.0	0.7732
+ARG	59	A	1.0	0.4849	0.5067	0.7882	1.0	0.7882	0.0	0.0	0.6475
+PRO	60	A	1.0	0.5275	0.466	0.5851	0.98	0.5734	0.0	0.0	0.5504
+GLU	61	A	1.0	0.4332	0.3348	0.5789	0.96	0.5557	0.0	0.0	0.4944
+GLU	62	A	1.0	0.4866	0.3348	0.772	1.0	0.772	0.0	0.0	0.6293
+ARG	63	A	1.0	0.5151	0.5067	0.7803	1.0	0.7803	0.0	0.0	0.6477
+PHE	64	A	0.8	0.699	1.0	0.8392	1.0	0.8392	0.0	0.0	0.9196
+PRO	65	A	0.8	0.7157	0.466	0.7796	1.0	0.7796	0.0	0.0	0.7476
+MET	66	A	0.8	0.8332	0.6606	0.7335	1.0	0.7335	0.0	0.0	0.7834
+MET	67	A	0.8	0.8131	0.6606	0.7926	1.0	0.7926	0.0	0.0	0.8029
+SER	68	A	1.0	0.8463	0.3574	0.9572	1.0	0.9572	0.6355	1.0	0.9018
+THR	69	A	0.5	0.9843	0.3257	0.8622	1.0	0.8622	0.0	0.0	0.9232
+PHE	70	A	0.8	0.8894	1.0	0.7921	1.0	0.7921	0.0	0.0	0.9447
+LYS	71	A	0.5	0.8959	0.2488	0.9589	1.0	0.9589	0.0	0.0	0.9274
+VAL	72	A	0.5	0.9561	0.5656	0.6351	1.0	0.6351	0.0	0.0	0.7956
+LEU	73	A	0.8	0.8761	0.7058	0.7186	1.0	0.7186	0.0	0.0	0.7974
+LEU	74	A	0.5	0.858	0.7058	0.7184	1.0	0.7184	0.0	0.0	0.7882
+CYS	75	A	0.5	0.8582	0.6425	0.7897	1.0	0.7897	0.0	0.0	0.824
+GLY	76	A	0.5	0.7779	0.4117	0.6851	1.0	0.6851	0.0	0.0	0.7315
+ALA	77	A	0.8	0.6935	0.3846	0.693	1.0	0.693	0.0	0.0	0.6932
+VAL	78	A	0.5	0.7046	0.5656	0.6326	1.0	0.6326	0.0	0.0	0.6686
+LEU	79	A	0.8	0.6453	0.7058	0.9168	1.0	0.9168	0.0	0.0	0.8113
+SER	80	A	1.0	0.5395	0.3574	0.5117	0.98	0.5015	0.0	0.0	0.5205
+ARG	81	A	1.0	0.4735	0.5067	0.6856	1.0	0.6856	0.0	0.0	0.5962
+VAL	82	A	1.0	0.4813	0.5656	0.7089	1.0	0.7089	0.0	0.0	0.6372
+ASP	83	A	1.0	0.4098	0.3212	0.8243	1.0	0.8243	0.0	0.0	0.617
+ALA	84	A	1.0	0.3341	0.3846	0.371	1.0	0.371	0.0	0.0	0.3778
+GLY	85	A	1.0	0.2913	0.4117	0.833	1.0	0.833	0.0	0.0	0.6224
+GLN	86	A	1.0	0.3254	0.4343	0.3336	0.96	0.3202	0.0	0.0	0.3798
+GLU	87	A	0.8	0.4682	0.3348	0.7056	1.0	0.7056	0.0	0.0	0.5869
+GLN	88	A	1.0	0.3582	0.4343	0.4124	1.0	0.4124	0.0	0.0	0.4234
+LEU	89	A	1.0	0.5127	0.7058	0.8865	1.0	0.8865	0.0	0.0	0.7961
+GLY	90	A	1.0	0.3832	0.4117	0.5267	0.9	0.4741	0.0	0.0	0.4429
+ARG	91	A	1.0	0.416	0.5067	0.6849	1.0	0.6849	0.0	0.0	0.5958
+ARG	92	A	1.0	0.3542	0.5067	0.6188	1.0	0.6188	0.0	0.0	0.5628
+ILE	93	A	1.0	0.5106	0.638	0.5855	0.98	0.5738	0.0	0.0	0.6059
+HIS	94	A	1.0	0.3345	0.5972	0.3589	0.8	0.2871	0.0	0.0	0.4658
+TYR	95	A	1.0	0.4788	0.7963	0.5885	1.0	0.5885	0.0	0.0	0.6924
+SER	96	A	1.0	0.3264	0.3574	0.3839	1.0	0.3839	0.0	0.0	0.3707
+GLN	97	A	1.0	0.2683	0.4343	0.3573	0.92	0.3287	0.0	0.0	0.3815
+ASN	98	A	1.0	0.2567	0.3936	0.3483	0.94	0.3274	0.0	0.0	0.3605
+ASP	99	A	1.0	0.4286	0.3212	0.7201	1.0	0.7201	0.0	0.0	0.5743
+LEU	100	A	1.0	0.4296	0.7058	0.7247	1.0	0.7247	0.6192	1.0	0.7152
+VAL	101	A	1.0	0.5086	0.5656	0.6393	1.0	0.6393	0.0	0.0	0.6024
+GLU	102	A	1.0	0.4648	0.3348	0.413	0.86	0.3552	0.0	0.0	0.41
+TYR	103	A	1.0	0.5424	0.7963	0.6543	1.0	0.6543	0.6695	1.0	0.7253
+SER	104	A	1.0	0.5235	0.3574	0.7693	1.0	0.7693	0.564	1.0	0.6464
+PRO	105	A	1.0	0.4902	0.466	0.8633	1.0	0.8633	0.6236	1.0	0.6768
+VAL	106	A	1.0	0.5153	0.5656	0.6077	1.0	0.6077	0.0	0.0	0.5866
+THR	107	A	0.5	0.5797	0.3257	0.7372	1.0	0.7372	0.0	0.0	0.6584
+GLU	108	A	1.0	0.3832	0.3348	0.5514	1.0	0.5514	0.0	0.0	0.4673
+LYS	109	A	1.0	0.33	0.2488	0.472	1.0	0.472	0.0	0.0	0.401
+HIS	110	A	1.0	0.4044	0.5972	0.597	1.0	0.597	0.0	0.0	0.5971
+LEU	111	A	1.0	0.3431	0.7058	0.5623	1.0	0.5623	0.0	0.0	0.634
+THR	112	A	1.0	0.2267	0.3257	0.6024	1.0	0.6024	0.0	0.0	0.464
+ASP	113	A	1.0	0.296	0.3212	0.4415	1.0	0.4415	0.0	0.0	0.3813
+GLY	114	A	0.8	0.4171	0.4117	0.7344	1.0	0.7344	0.0	0.0	0.5758
+MET	115	A	0.8	0.5403	0.6606	0.668	1.0	0.668	0.0	0.0	0.6643
+THR	116	A	1.0	0.4768	0.3257	0.6601	1.0	0.6601	0.0	0.0	0.5684
+VAL	117	A	0.5	0.6126	0.5656	0.5921	1.0	0.5921	0.0	0.0	0.6023
+ARG	118	A	1.0	0.4881	0.5067	0.4469	1.0	0.4469	0.0	0.0	0.4974
+GLU	119	A	1.0	0.5229	0.3348	0.6054	1.0	0.6054	0.0	0.0	0.5642
+LEU	120	A	0.5	0.7037	0.7058	0.8074	1.0	0.8074	0.0	0.0	0.7566
+CYS	121	A	0.5	0.7749	0.6425	0.8041	1.0	0.8041	0.0	0.0	0.7895
+SER	122	A	1.0	0.6332	0.3574	0.5345	0.98	0.5238	0.0	0.0	0.5785
+ALA	123	A	0.8	0.6798	0.3846	0.8645	1.0	0.8645	0.0	0.0	0.7722
+ALA	124	A	0.5	0.8333	0.3846	0.7104	1.0	0.7104	0.0	0.0	0.7718
+ILE	125	A	0.5	0.815	0.638	0.6368	1.0	0.6368	0.0	0.0	0.7265
+THR	126	A	1.0	0.6349	0.3257	0.667	1.0	0.667	0.0	0.0	0.651
+MET	127	A	1.0	0.5665	0.6606	0.5067	0.98	0.4966	0.0	0.0	0.6136
+SER	128	A	1.0	0.7294	0.3574	0.9486	1.0	0.9486	0.6312	1.0	0.839
+ASP	129	A	0.5	0.694	0.3212	0.9405	1.0	0.9405	0.0	0.0	0.8172
+ASN	130	A	1.0	0.674	0.3936	0.8905	1.0	0.8905	0.6312	1.0	0.7822
+THR	131	A	0.8	0.6281	0.3257	0.6701	1.0	0.6701	0.0	0.0	0.6491
+ALA	132	A	0.5	0.7599	0.3846	0.902	1.0	0.902	0.0	0.0	0.831
+ALA	133	A	0.5	0.8236	0.3846	0.7275	1.0	0.7275	0.0	0.0	0.7756
+ASN	134	A	1.0	0.6487	0.3936	0.9255	1.0	0.9255	0.6217	1.0	0.7871
+LEU	135	A	1.0	0.6292	0.7058	0.7598	1.0	0.7598	0.0	0.0	0.7328
+LEU	136	A	0.5	0.7834	0.7058	0.8068	1.0	0.8068	0.0	0.0	0.7951
+LEU	137	A	0.5	0.6911	0.7058	0.7842	1.0	0.7842	0.0	0.0	0.745
+THR	138	A	1.0	0.505	0.3257	0.4486	0.88	0.3948	0.0	0.0	0.4499
+THR	139	A	1.0	0.5607	0.3257	0.5776	0.92	0.5313	0.0	0.0	0.546
+ILE	140	A	1.0	0.593	0.638	0.58	0.98	0.5684	0.0	0.0	0.6155
+GLY	141	A	1.0	0.4358	0.4117	0.9101	1.0	0.9101	0.0	0.0	0.673
+GLY	142	A	0.8	0.5189	0.4117	0.92	1.0	0.92	0.0	0.0	0.7194
+PRO	143	A	1.0	0.5518	0.466	0.8312	1.0	0.8312	0.0	0.0	0.6915
+LYS	144	A	1.0	0.354	0.2488	0.4453	0.94	0.4186	0.0	0.0	0.3863
+GLU	145	A	1.0	0.4377	0.3348	0.5495	1.0	0.5495	0.0	0.0	0.4936
+LEU	146	A	0.8	0.6906	0.7058	0.6933	1.0	0.6933	0.0	0.0	0.6996
+THR	147	A	1.0	0.52	0.3257	0.788	1.0	0.788	0.0	0.0	0.654
+ALA	148	A	1.0	0.4216	0.3846	0.5145	1.0	0.5145	0.0	0.0	0.468
+PHE	149	A	1.0	0.5765	1.0	0.7179	1.0	0.7179	0.0	0.0	0.859
+LEU	150	A	0.5	0.636	0.7058	0.6156	1.0	0.6156	0.0	0.0	0.6709
+HIS	151	A	1.0	0.3909	0.5972	0.7796	1.0	0.7796	0.0	0.0	0.6884
+ASN	152	A	1.0	0.3704	0.3936	0.4439	0.96	0.4262	0.0	0.0	0.4099
+MET	153	A	1.0	0.522	0.6606	0.562	0.96	0.5395	0.0	0.0	0.6
+GLY	154	A	1.0	0.4098	0.4117	0.901	1.0	0.901	0.0	0.0	0.6564
+ASP	155	A	0.8	0.5428	0.3212	0.8998	1.0	0.8998	0.0	0.0	0.7213
+HIS	156	A	1.0	0.3581	0.5972	0.3194	0.98	0.3131	0.0	0.0	0.4776
+VAL	157	A	1.0	0.4988	0.5656	0.4669	0.98	0.4576	0.0	0.0	0.5322
+THR	158	A	0.8	0.6713	0.3257	0.7055	1.0	0.7055	0.0	0.0	0.7055
+ARG	159	A	1.0	0.5047	0.5067	0.8208	1.0	0.8208	0.0	0.0	0.8208
+LEU	160	A	0.8	0.6849	0.7058	0.7638	1.0	0.7638	0.0	0.0	0.7638
+ASP	161	A	1.0	0.5004	0.3212	0.8324	1.0	0.8324	0.0	0.0	0.8324
+ARG	162	A	1.0	0.4994	0.5067	0.8001	1.0	0.8001	0.0	0.0	0.8001
+TRP	163	A	1.0	0.5305	0.9909	0.4471	0.96	0.4292	0.6565	1.0	0.4292
+GLU	164	A	0.8	0.675	0.3348	0.8706	1.0	0.8706	0.0	0.0	0.7728
+PRO	165	A	1.0	0.5174	0.466	0.681	1.0	0.681	0.0	0.0	0.5992
+GLU	166	A	1.0	0.4656	0.3348	0.472	0.9	0.4248	0.0	0.0	0.4452
+LEU	167	A	0.8	0.6894	0.7058	0.8229	1.0	0.8229	0.0	0.0	0.7644
+ASN	168	A	1.0	0.6465	0.3936	0.8211	1.0	0.8211	0.5738	1.0	0.7338
+GLU	169	A	1.0	0.4575	0.3348	0.5883	1.0	0.5883	0.0	0.0	0.5229
+ALA	170	A	1.0	0.5691	0.3846	0.674	1.0	0.674	0.0	0.0	0.6216
+ILE	171	A	1.0	0.3772	0.638	0.3896	0.98	0.3818	0.0	0.0	0.5099
+PRO	172	A	1.0	0.3669	0.466	0.7768	1.0	0.7768	0.0	0.0	0.6214
+ASN	173	A	1.0	0.336	0.3936	0.6994	1.0	0.6994	0.0	0.0	0.5465
+ASP	174	A	1.0	0.4217	0.3212	0.8039	1.0	0.8039	0.0	0.0	0.6128
+GLU	175	A	1.0	0.4207	0.3348	0.579	0.96	0.5559	0.0	0.0	0.4883
+ARG	176	A	1.0	0.423	0.5067	0.7876	1.0	0.7876	0.0	0.0	0.6472
+ASP	177	A	0.8	0.6535	0.3212	0.918	1.0	0.918	0.0	0.0	0.7857
+THR	178	A	1.0	0.6457	0.3257	0.8561	1.0	0.8561	0.0	0.0	0.7509
+THR	179	A	0.5	0.7536	0.3257	0.8062	1.0	0.8062	0.0	0.0	0.7799
+MET	180	A	1.0	0.5708	0.6606	0.7298	1.0	0.7298	0.0	0.0	0.6952
+PRO	181	A	0.5	0.723	0.466	0.8848	1.0	0.8848	0.0	0.0	0.8039
+ALA	182	A	1.0	0.598	0.3846	0.4338	0.96	0.4164	0.0	0.0	0.5072
+ALA	183	A	1.0	0.6268	0.3846	0.809	1.0	0.809	0.0	0.0	0.7179
+MET	184	A	0.5	0.8376	0.6606	0.7792	1.0	0.7792	0.0	0.0	0.8084
+ALA	185	A	0.5	0.7466	0.3846	0.5576	1.0	0.5576	0.0	0.0	0.6521
+THR	186	A	1.0	0.584	0.3257	0.4016	0.84	0.3373	0.0	0.0	0.4606
+THR	187	A	0.8	0.7083	0.3257	0.735	1.0	0.735	0.0	0.0	0.7216
+LEU	188	A	0.5	0.846	0.7058	0.8024	1.0	0.8024	0.0	0.0	0.8242
+ARG	189	A	1.0	0.5527	0.5067	0.4245	0.96	0.4075	0.0	0.0	0.5297
+LYS	190	A	1.0	0.5328	0.2488	0.392	1.0	0.392	0.0	0.0	0.4624
+LEU	191	A	0.5	0.7328	0.7058	0.7264	1.0	0.7264	0.0	0.0	0.7296
+LEU	192	A	0.8	0.7139	0.7058	0.629	1.0	0.629	0.0	0.0	0.7098
+THR	193	A	1.0	0.5278	0.3257	0.5915	1.0	0.5915	0.0	0.0	0.5596
+GLY	194	A	1.0	0.478	0.4117	0.8133	1.0	0.8133	0.0	0.0	0.6457
+GLU	195	A	1.0	0.3446	0.3348	0.4892	0.9	0.4403	0.0	0.0	0.3924
+LEU	196	A	1.0	0.5054	0.7058	0.4992	0.92	0.4593	0.0	0.0	0.6056
+LEU	197	A	0.8	0.5703	0.7058	0.9434	1.0	0.9434	0.0	0.0	0.8246
+THR	198	A	1.0	0.3877	0.3257	0.5824	1.0	0.5824	0.0	0.0	0.485
+LEU	199	A	1.0	0.3445	0.7058	0.3969	0.8	0.3175	0.0	0.0	0.5252
+ALA	200	A	1.0	0.386	0.3846	0.4251	0.98	0.4166	0.0	0.0	0.4013
+SER	201	A	0.8	0.5245	0.3574	0.8076	1.0	0.8076	0.0	0.0	0.666
+ARG	202	A	1.0	0.4966	0.5067	0.7406	1.0	0.7406	0.0	0.0	0.6236
+GLN	203	A	1.0	0.4657	0.4343	0.3721	0.8	0.2977	0.0	0.0	0.45
+GLN	204	A	1.0	0.5485	0.4343	0.5601	1.0	0.5601	0.0	0.0	0.5543
+LEU	205	A	0.5	0.7577	0.7058	0.8828	1.0	0.8828	0.0	0.0	0.8202
+ILE	206	A	1.0	0.6366	0.638	0.4625	0.92	0.4255	0.0	0.0	0.6373
+ASP	207	A	1.0	0.5326	0.3212	0.4118	0.94	0.3871	0.0	0.0	0.4598
+TRP	208	A	0.8	0.6672	0.9909	0.8299	1.0	0.8299	0.0	0.0	0.9104
+MET	209	A	0.5	0.7957	0.6606	0.7864	1.0	0.7864	0.0	0.0	0.791
+GLU	210	A	1.0	0.5437	0.3348	0.3948	1.0	0.3948	0.0	0.0	0.4692
+ALA	211	A	1.0	0.5428	0.3846	0.5405	0.96	0.5189	0.0	0.0	0.5308
+ASP	212	A	1.0	0.6481	0.3212	0.6863	1.0	0.6863	0.0	0.0	0.6672
+LYS	213	A	1.0	0.474	0.2488	0.4409	0.96	0.4233	0.0	0.0	0.4486
+VAL	214	A	1.0	0.6057	0.5656	0.8586	1.0	0.8586	0.6338	1.0	0.7322
+ALA	215	A	0.5	0.6521	0.3846	0.848	1.0	0.848	0.0	0.0	0.75
+GLY	216	A	1.0	0.5019	0.4117	0.556	1.0	0.556	0.0	0.0	0.529
+PRO	217	A	1.0	0.4821	0.466	0.4396	1.0	0.4396	0.0	0.0	0.474
+LEU	218	A	0.5	0.6631	0.7058	0.7855	1.0	0.7855	0.0	0.0	0.7456
+LEU	219	A	0.8	0.7409	0.7058	0.7473	1.0	0.7473	0.0	0.0	0.7441
+ARG	220	A	1.0	0.5678	0.5067	0.8248	1.0	0.8248	0.0	0.0	0.6963
+SER	221	A	1.0	0.4591	0.3574	0.7973	1.0	0.7973	0.0	0.0	0.6282
+ALA	222	A	1.0	0.4909	0.3846	0.7543	1.0	0.7543	0.0	0.0	0.6226
+LEU	223	A	1.0	0.5015	0.7058	0.7806	0.98	0.765	0.0	0.0	0.7354
+PRO	224	A	1.0	0.3538	0.466	0.8972	1.0	0.8972	0.0	0.0	0.6816
+ALA	225	A	1.0	0.2464	0.3846	0.3912	0.88	0.3442	0.0	0.0	0.3644
+GLY	226	A	1.0	0.2821	0.4117	0.5641	1.0	0.5641	0.0	0.0	0.4879
+TRP	227	A	1.0	0.4327	0.9909	0.8583	1.0	0.8583	0.0	0.0	0.9246
+PHE	228	A	1.0	0.5177	1.0	0.4604	0.96	0.442	0.0	0.0	0.7588
+ILE	229	A	1.0	0.628	0.638	0.7273	1.0	0.7273	0.0	0.0	0.6826
+ALA	230	A	0.5	0.7157	0.3846	0.7834	1.0	0.7834	0.0	0.0	0.7495
+ASP	231	A	0.5	0.78	0.3212	0.8777	1.0	0.8777	0.0	0.0	0.8288
+LYS	232	A	0.5	0.8575	0.2488	0.8946	1.0	0.8946	0.0	0.0	0.876
+SER	233	A	0.8	0.793	0.3574	0.8829	1.0	0.8829	0.0	0.0	0.838
+GLY	234	A	0.8	0.8195	0.4117	0.9476	1.0	0.9476	0.0	0.0	0.8836
+ALA	235	A	1.0	0.6882	0.3846	0.6626	1.0	0.6626	0.0	0.0	0.6754
+GLY	236	A	1.0	0.6274	0.4117	0.7509	1.0	0.7509	0.5643	1.0	0.6891
+GLU	237	A	1.0	0.482	0.3348	0.4952	0.94	0.4654	0.0	0.0	0.4737
+ARG	238	A	1.0	0.4196	0.5067	0.585	1.0	0.585	0.0	0.0	0.5458
+GLY	239	A	1.0	0.5384	0.4117	0.7475	1.0	0.7475	0.0	0.0	0.643
+SER	240	A	0.8	0.6602	0.3574	0.6542	1.0	0.6542	0.0	0.0	0.6572
+ARG	241	A	1.0	0.7045	0.5067	0.5641	1.0	0.5641	0.0	0.0	0.6343
+GLY	242	A	0.5	0.8695	0.4117	0.8193	1.0	0.8193	0.0	0.0	0.8444
+ILE	243	A	0.5	0.8867	0.638	0.8821	1.0	0.8821	0.0	0.0	0.8844
+ILE	244	A	0.5	1.0	0.638	0.6077	1.0	0.6077	0.0	0.0	0.819
+ALA	245	A	0.5	0.8736	0.3846	0.832	1.0	0.832	0.0	0.0	0.8528
+ALA	246	A	0.5	0.7637	0.3846	0.5933	1.0	0.5933	0.0	0.0	0.6785
+LEU	247	A	0.8	0.6955	0.7058	0.522	0.98	0.5116	0.0	0.0	0.7006
+GLY	248	A	0.5	0.5269	0.4117	0.7481	1.0	0.7481	0.0	0.0	0.6375
+PRO	249	A	1.0	0.3818	0.466	0.8488	1.0	0.8488	0.0	0.0	0.6574
+ASP	250	A	1.0	0.2685	0.3212	0.7141	0.98	0.6998	0.0	0.0	0.5105
+GLY	251	A	1.0	0.3519	0.4117	0.7147	0.96	0.6861	0.0	0.0	0.5489
+LYS	252	A	1.0	0.3777	0.2488	0.557	0.96	0.5347	0.0	0.0	0.4562
+PRO	253	A	1.0	0.5517	0.466	0.4431	0.94	0.4165	0.0	0.0	0.5088
+SER	254	A	1.0	0.5022	0.3574	0.7783	1.0	0.7783	0.0	0.0	0.6402
+ARG	255	A	1.0	0.5697	0.5067	0.5295	1.0	0.5295	0.0	0.0	0.5496
+ILE	256	A	0.5	0.7646	0.638	0.6104	1.0	0.6104	0.0	0.0	0.7013
+VAL	257	A	0.5	0.8492	0.5656	0.5592	1.0	0.5592	0.0	0.0	0.7074
+VAL	258	A	0.5	0.9025	0.5656	0.5984	1.0	0.5984	0.0	0.0	0.7505
+ILE	259	A	0.5	0.8927	0.638	0.6416	1.0	0.6416	0.0	0.0	0.7672
+TYR	260	A	0.8	0.8772	0.7963	0.7728	1.0	0.7728	0.0	0.0	0.8368
+THR	261	A	0.8	0.7217	0.3257	0.6266	1.0	0.6266	0.0	0.0	0.6742
+THR	262	A	1.0	0.6203	0.3257	0.595	1.0	0.595	0.0	0.0	0.6076
+GLY	263	A	1.0	0.4815	0.4117	0.5253	0.94	0.4938	0.0	0.0	0.4876
+SER	264	A	0.8	0.4788	0.3574	0.5525	0.98	0.5414	0.0	0.0	0.5101
+GLN	265	A	1.0	0.3055	0.4343	0.3663	0.58	0.2124	0.0	0.0	0.3699
+ALA	266	A	1.0	0.3944	0.3846	0.5192	1.0	0.5192	0.0	0.0	0.4568
+THR	267	A	1.0	0.322	0.3257	0.4979	0.9	0.4481	0.0	0.0	0.3869
+MET	268	A	1.0	0.4751	0.6606	0.5062	1.0	0.5062	0.5384	1.0	0.5834
+ASP	269	A	1.0	0.3583	0.3212	0.401	0.96	0.3849	0.0	0.0	0.3716
+GLU	270	A	1.0	0.3681	0.3348	0.4038	0.96	0.3876	0.0	0.0	0.3778
+ARG	271	A	1.0	0.5589	0.5067	0.6372	1.0	0.6372	0.0	0.0	0.598
+ASN	272	A	1.0	0.5374	0.3936	0.5862	1.0	0.5862	0.0	0.0	0.5618
+ARG	273	A	1.0	0.3798	0.5067	0.5628	0.98	0.5516	0.0	0.0	0.5292
+GLN	274	A	1.0	0.5361	0.4343	0.5753	0.98	0.5638	0.0	0.0	0.5499
+ILE	275	A	0.5	0.7372	0.638	0.6805	1.0	0.6805	0.0	0.0	0.7088
+ALA	276	A	1.0	0.5733	0.3846	0.7999	1.0	0.7999	0.0	0.0	0.6866
+GLU	277	A	1.0	0.4906	0.3348	0.4883	0.84	0.4102	0.0	0.0	0.4504
+ILE	278	A	0.8	0.7031	0.638	0.6801	1.0	0.6801	0.0	0.0	0.6916
+GLY	279	A	0.5	0.6544	0.4117	0.6752	1.0	0.6752	0.0	0.0	0.6648
+ALA	280	A	1.0	0.4945	0.3846	0.6462	1.0	0.6462	0.0	0.0	0.5704
+SER	281	A	1.0	0.5238	0.3574	0.5353	0.9	0.4817	0.0	0.0	0.5028
+LEU	282	A	0.8	0.6582	0.7058	0.5349	0.98	0.5242	0.0	0.0	0.682
+ILE	283	A	1.0	0.508	0.638	0.4816	0.98	0.472	0.0	0.0	0.573
+LYS	284	A	1.0	0.3538	0.2488	0.3331	0.68	0.2265	0.0	0.0	0.3013
+HIS	285	A	1.0	0.4294	0.5972	0.1371	0.46	0.063	0.0	0.0	0.5133
+TRP	286	A	1.0	0.4871	0.9909	0.2251	0.74	0.1666	0.0	0.0	0.739

example/example-esgemme-script.sh → examples/example-esgemme-script.sh

@@ -17,8 +17,8 @@ then
     # In ../tests folder, you can find a sample JET2 file called BLAT_jet.res 
     echo "Running ESGEMME with a user-provided alignment file."
     echo "Using a previously produced prot_jet.res file to check reproducibility!"
-    cp ../tests/BLAT_jet.res .
-    python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --jetfile BLAT_jet.res
+
+    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta --jetfile ../data/BLAT_jet.res
 
 elif [ "$1" == "withpdb" ]
 then
@@ -26,7 +26,8 @@ then
     #Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
     echo "Using blat-af2.pdb for the structural feature calculations!"
     echo "Entire mutational map of the protein will be calculated!"
-    python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc
+    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
+	   --pdbfile ../data/blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc
 
 elif [ "$1" == "withpdb-withmutfile" ]
 then
@@ -34,7 +35,9 @@ then
     #Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
     echo "Using blat-af2.pdb for the structural feature calculations!"
     echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
-    python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc -m Stiffler_2015_BLAT_ECOLX.mut
+    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta  \
+	   --pdbfile ../data/blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc \
+	   -m ../data/Stiffler_2015_BLAT_ECOLX.mut
 
 elif [ "$1" == "ssjetormax" ]
 then
@@ -42,11 +45,13 @@ then
     #Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
     echo "Using blat-af2.pdb for the secondary structure based calculations!"
     echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
-    python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb --normweightmode ssjetormax -m Stiffler_2015_BLAT_ECOLX.mut
+    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
+	   --pdbfile ../data/blat-af2.pdb --normweightmode ssjetormax \
+	   -m ../data/Stiffler_2015_BLAT_ECOLX.mut
     
 else
     echo "Running EGEMME with a user-provided alignment file."
     echo "Since a pdb file is not provided, only evolutionary information will be used!"
-    python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
+    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta
     
 fi

pred.R

@@ -174,7 +174,7 @@ computePSSM2<-function(mat){
 }
 
 computeNbSeqsAlph<-function(nbSeqs,alphabet){
-	path=paste(Sys.getenv("ESGEMME_PATH"),"/alphabets/",sep="")
+	path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
         AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
         facAA = rep(NA,20)
         for(Let in AA){
@@ -210,7 +210,7 @@ readMut<-function(fname){
 }
 
 which.class<-function(a,alphabet){
-        path=paste(Sys.getenv("ESGEMME_PATH"),"/alphabets/",sep="")
+        path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
         AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
         for(Let in AA){
                 Let = toString(Let)