Convert Grantham Amino Acid matrix into Python dict.

grantham-dict.py

#!/usr/bin/env python
import sys
import pprint

def make_grantham_dict(grantham_mat_file):

        """
	Citation:   http://www.ncbi.nlm.nih.gov/pubmed/4843792
	Provenance: http://www.genome.jp/dbget-bin/www_bget?aaindex:GRAR740104

	.	A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V
	A	0	112	111	126	195	91	107	60	86	94	96	106	84	113	27	99	58	148	112	64
	R	112	0	86	96	180	43	54	125	29	97	102	26	91	97	103	110	71	101	77	96
	N	111	86	0	23	139	46	42	80	68	149	153	94	142	158	91	46	65	174	143	133
	D	126	96	23	0	154	61	45	94	81	168	172	101	160	177	108	65	85	181	160	152
	C	195	180	139	154	0	154	170	159	174	198	198	202	196	205	169	112	149	215	194	192
	Q	91	43	46	61	154	0	29	87	24	109	113	53	101	116	76	68	42	130	99	96
	E	107	54	42	45	170	29	0	98	40	134	138	56	126	140	93	80	65	152	122	121
	G	60	125	80	94	159	87	98	0	98	135	138	127	127	153	42	56	59	184	147	109
	H	86	29	68	81	174	24	40	98	0	94	99	32	87	100	77	89	47	115	83	84
	I	94	97	149	168	198	109	134	135	94	0	5	102	10	21	95	142	89	61	33	29
	L	96	102	153	172	198	113	138	138	99	5	0	107	15	22	98	145	92	61	36	32
	K	106	26	94	101	202	53	56	127	32	102	107	0	95	102	103	121	78	110	85	97
	M	84	91	142	160	196	101	126	127	87	10	15	95	0	28	87	135	81	67	36	21
	F	113	97	158	177	205	116	140	153	100	21	22	102	28	0	114	155	103	40	22	50
	P	27	103	91	108	169	76	93	42	77	95	98	103	87	114	0	74	38	147	110	68
	S	99	110	46	65	112	68	80	56	89	142	145	121	135	155	74	0	58	177	144	124
	T	58	71	65	85	149	42	65	59	47	89	92	78	81	103	38	58	0	128	92	69
	W	148	101	174	181	215	130	152	184	115	61	61	110	67	40	147	177	128	0	37	88
	Y	112	77	143	160	194	99	122	147	83	33	36	85	36	22	110	144	92	37	0	55
	V	64	96	133	152	192	96	121	109	84	29	32	97	21	50	68	124	69	88	55	0

	"""

	f = open(grantham_mat_file)

	header = f.next().strip().split('\t')
	idx_to_aa = dict(zip(range(0,len(header)), header))


	grantham_dict = {}
	for line in f:
		fields = line.strip().split('\t')
		from_aa = fields[0]

		for idx, score in enumerate(fields):
			if idx == 0:
				continue
			to_aa = idx_to_aa[idx]
			grantham_dict[(from_aa, to_aa)] = score

	return grantham_dict

if __name__ == "__main__":
    grantham_dict = make_grantham_dict(sys.argv[1])

    pp = pprint.PrettyPrinter(indent=2)
    pp.pprint(grantham_dict)

grantham.matrix.txt

. A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V
A	0	112	111	126	195	91	107	60	86	94	96	106	84	113	27	99	58	148	112	64
R	112	0	86	96	180	43	54	125	29	97	102	26	91	97	103	110	71	101	77	96
N	111	86	0	23	139	46	42	80	68	149	153	94	142	158	91	46	65	174	143	133
D	126	96	23	0	154	61	45	94	81	168	172	101	160	177	108	65	85	181	160	152
C	195	180	139	154	0	154	170	159	174	198	198	202	196	205	169	112	149	215	194	192
Q	91	43	46	61	154	0	29	87	24	109	113	53	101	116	76	68	42	130	99	96
E	107	54	42	45	170	29	0	98	40	134	138	56	126	140	93	80	65	152	122	121
G	60	125	80	94	159	87	98	0	98	135	138	127	127	153	42	56	59	184	147	109
H	86	29	68	81	174	24	40	98	0	94	99	32	87	100	77	89	47	115	83	84
I	94	97	149	168	198	109	134	135	94	0	5	102	10	21	95	142	89	61	33	29
L	96	102	153	172	198	113	138	138	99	5	0	107	15	22	98	145	92	61	36	32
K	106	26	94	101	202	53	56	127	32	102	107	0	95	102	103	121	78	110	85	97
M	84	91	142	160	196	101	126	127	87	10	15	95	0	28	87	135	81	67	36	21
F	113	97	158	177	205	116	140	153	100	21	22	102	28	0	114	155	103	40	22	50
P	27	103	91	108	169	76	93	42	77	95	98	103	87	114	0	74	38	147	110	68
S	99	110	46	65	112	68	80	56	89	142	145	121	135	155	74	0	58	177	144	124
T	58	71	65	85	149	42	65	59	47	89	92	78	81	103	38	58	0	128	92	69
W	148	101	174	181	215	130	152	184	115	61	61	110	67	40	147	177	128	0	37	88
Y	112	77	143	160	194	99	122	147	83	33	36	85	36	22	110	144	92	37	0	55
V	64	96	133	152	192	96	121	109	84	29	32	97	21	50	68	124	69	88	55	0

log.sh

$ python grantham-dict.py grantham.matrix.txt

{ ('A', 'A'): '0',
  ('A', 'C'): '195',
  ('A', 'D'): '126',
  ('A', 'E'): '107',
  ('A', 'F'): '113',
  ('A', 'G'): '60',
  ('A', 'H'): '86',
  ('A', 'I'): '94',
  ('A', 'K'): '106',
  ('A', 'L'): '96',
  ('A', 'M'): '84',
  ('A', 'N'): '111',
  ('A', 'P'): '27',
  ('A', 'Q'): '91',
  ('A', 'R'): '112',
  ('A', 'S'): '99',
  ('A', 'T'): '58',
  ('A', 'V'): '64',
  ('A', 'W'): '148',
  ('A', 'Y'): '112',
  ('C', 'A'): '195',
  ('C', 'C'): '0',
  ('C', 'D'): '154',
  ('C', 'E'): '170',
  ('C', 'F'): '205',
  ('C', 'G'): '159',
  ('C', 'H'): '174',
  ('C', 'I'): '198',
  ('C', 'K'): '202',
  ('C', 'L'): '198',
  ('C', 'M'): '196',
  ('C', 'N'): '139',
  ('C', 'P'): '169',
  ('C', 'Q'): '154',
  ('C', 'R'): '180',
  ('C', 'S'): '112',
  ('C', 'T'): '149',
  ('C', 'V'): '192',
  ('C', 'W'): '215',
  ('C', 'Y'): '194',
  ('D', 'A'): '126',
  ('D', 'C'): '154',
  ('D', 'D'): '0',
  ('D', 'E'): '45',
  ('D', 'F'): '177',
  ('D', 'G'): '94',
  ('D', 'H'): '81',
  ('D', 'I'): '168',
  ('D', 'K'): '101',
  ('D', 'L'): '172',
  ('D', 'M'): '160',
  ('D', 'N'): '23',
  ('D', 'P'): '108',
  ('D', 'Q'): '61',
  ('D', 'R'): '96',
  ('D', 'S'): '65',
  ('D', 'T'): '85',
  ('D', 'V'): '152',
  ('D', 'W'): '181',
  ('D', 'Y'): '160',
  ('E', 'A'): '107',
  ('E', 'C'): '170',
  ('E', 'D'): '45',
  ('E', 'E'): '0',
  ('E', 'F'): '140',
  ('E', 'G'): '98',
  ('E', 'H'): '40',
  ('E', 'I'): '134',
  ('E', 'K'): '56',
  ('E', 'L'): '138',
  ('E', 'M'): '126',
  ('E', 'N'): '42',
  ('E', 'P'): '93',
  ('E', 'Q'): '29',
  ('E', 'R'): '54',
  ('E', 'S'): '80',
  ('E', 'T'): '65',
  ('E', 'V'): '121',
  ('E', 'W'): '152',
  ('E', 'Y'): '122',
  ('F', 'A'): '113',
  ('F', 'C'): '205',
  ('F', 'D'): '177',
  ('F', 'E'): '140',
  ('F', 'F'): '0',
  ('F', 'G'): '153',
  ('F', 'H'): '100',
  ('F', 'I'): '21',
  ('F', 'K'): '102',
  ('F', 'L'): '22',
  ('F', 'M'): '28',
  ('F', 'N'): '158',
  ('F', 'P'): '114',
  ('F', 'Q'): '116',
  ('F', 'R'): '97',
  ('F', 'S'): '155',
  ('F', 'T'): '103',
  ('F', 'V'): '50',
  ('F', 'W'): '40',
  ('F', 'Y'): '22',
  ('G', 'A'): '60',
  ('G', 'C'): '159',
  ('G', 'D'): '94',
  ('G', 'E'): '98',
  ('G', 'F'): '153',
  ('G', 'G'): '0',
  ('G', 'H'): '98',
  ('G', 'I'): '135',
  ('G', 'K'): '127',
  ('G', 'L'): '138',
  ('G', 'M'): '127',
  ('G', 'N'): '80',
  ('G', 'P'): '42',
  ('G', 'Q'): '87',
  ('G', 'R'): '125',
  ('G', 'S'): '56',
  ('G', 'T'): '59',
  ('G', 'V'): '109',
  ('G', 'W'): '184',
  ('G', 'Y'): '147',
  ('H', 'A'): '86',
  ('H', 'C'): '174',
  ('H', 'D'): '81',
  ('H', 'E'): '40',
  ('H', 'F'): '100',
  ('H', 'G'): '98',
  ('H', 'H'): '0',
  ('H', 'I'): '94',
  ('H', 'K'): '32',
  ('H', 'L'): '99',
  ('H', 'M'): '87',
  ('H', 'N'): '68',
  ('H', 'P'): '77',
  ('H', 'Q'): '24',
  ('H', 'R'): '29',
  ('H', 'S'): '89',
  ('H', 'T'): '47',
  ('H', 'V'): '84',
  ('H', 'W'): '115',
  ('H', 'Y'): '83',
  ('I', 'A'): '94',
  ('I', 'C'): '198',
  ('I', 'D'): '168',
  ('I', 'E'): '134',
  ('I', 'F'): '21',
  ('I', 'G'): '135',
  ('I', 'H'): '94',
  ('I', 'I'): '0',
  ('I', 'K'): '102',
  ('I', 'L'): '5',
  ('I', 'M'): '10',
  ('I', 'N'): '149',
  ('I', 'P'): '95',
  ('I', 'Q'): '109',
  ('I', 'R'): '97',
  ('I', 'S'): '142',
  ('I', 'T'): '89',
  ('I', 'V'): '29',
  ('I', 'W'): '61',
  ('I', 'Y'): '33',
  ('K', 'A'): '106',
  ('K', 'C'): '202',
  ('K', 'D'): '101',
  ('K', 'E'): '56',
  ('K', 'F'): '102',
  ('K', 'G'): '127',
  ('K', 'H'): '32',
  ('K', 'I'): '102',
  ('K', 'K'): '0',
  ('K', 'L'): '107',
  ('K', 'M'): '95',
  ('K', 'N'): '94',
  ('K', 'P'): '103',
  ('K', 'Q'): '53',
  ('K', 'R'): '26',
  ('K', 'S'): '121',
  ('K', 'T'): '78',
  ('K', 'V'): '97',
  ('K', 'W'): '110',
  ('K', 'Y'): '85',
  ('L', 'A'): '96',
  ('L', 'C'): '198',
  ('L', 'D'): '172',
  ('L', 'E'): '138',
  ('L', 'F'): '22',
  ('L', 'G'): '138',
  ('L', 'H'): '99',
  ('L', 'I'): '5',
  ('L', 'K'): '107',
  ('L', 'L'): '0',
  ('L', 'M'): '15',
  ('L', 'N'): '153',
  ('L', 'P'): '98',
  ('L', 'Q'): '113',
  ('L', 'R'): '102',
  ('L', 'S'): '145',
  ('L', 'T'): '92',
  ('L', 'V'): '32',
  ('L', 'W'): '61',
  ('L', 'Y'): '36',
  ('M', 'A'): '84',
  ('M', 'C'): '196',
  ('M', 'D'): '160',
  ('M', 'E'): '126',
  ('M', 'F'): '28',
  ('M', 'G'): '127',
  ('M', 'H'): '87',
  ('M', 'I'): '10',
  ('M', 'K'): '95',
  ('M', 'L'): '15',
  ('M', 'M'): '0',
  ('M', 'N'): '142',
  ('M', 'P'): '87',
  ('M', 'Q'): '101',
  ('M', 'R'): '91',
  ('M', 'S'): '135',
  ('M', 'T'): '81',
  ('M', 'V'): '21',
  ('M', 'W'): '67',
  ('M', 'Y'): '36',
  ('N', 'A'): '111',
  ('N', 'C'): '139',
  ('N', 'D'): '23',
  ('N', 'E'): '42',
  ('N', 'F'): '158',
  ('N', 'G'): '80',
  ('N', 'H'): '68',
  ('N', 'I'): '149',
  ('N', 'K'): '94',
  ('N', 'L'): '153',
  ('N', 'M'): '142',
  ('N', 'N'): '0',
  ('N', 'P'): '91',
  ('N', 'Q'): '46',
  ('N', 'R'): '86',
  ('N', 'S'): '46',
  ('N', 'T'): '65',
  ('N', 'V'): '133',
  ('N', 'W'): '174',
  ('N', 'Y'): '143',
  ('P', 'A'): '27',
  ('P', 'C'): '169',
  ('P', 'D'): '108',
  ('P', 'E'): '93',
  ('P', 'F'): '114',
  ('P', 'G'): '42',
  ('P', 'H'): '77',
  ('P', 'I'): '95',
  ('P', 'K'): '103',
  ('P', 'L'): '98',
  ('P', 'M'): '87',
  ('P', 'N'): '91',
  ('P', 'P'): '0',
  ('P', 'Q'): '76',
  ('P', 'R'): '103',
  ('P', 'S'): '74',
  ('P', 'T'): '38',
  ('P', 'V'): '68',
  ('P', 'W'): '147',
  ('P', 'Y'): '110',
  ('Q', 'A'): '91',
  ('Q', 'C'): '154',
  ('Q', 'D'): '61',
  ('Q', 'E'): '29',
  ('Q', 'F'): '116',
  ('Q', 'G'): '87',
  ('Q', 'H'): '24',
  ('Q', 'I'): '109',
  ('Q', 'K'): '53',
  ('Q', 'L'): '113',
  ('Q', 'M'): '101',
  ('Q', 'N'): '46',
  ('Q', 'P'): '76',
  ('Q', 'Q'): '0',
  ('Q', 'R'): '43',
  ('Q', 'S'): '68',
  ('Q', 'T'): '42',
  ('Q', 'V'): '96',
  ('Q', 'W'): '130',
  ('Q', 'Y'): '99',
  ('R', 'A'): '112',
  ('R', 'C'): '180',
  ('R', 'D'): '96',
  ('R', 'E'): '54',
  ('R', 'F'): '97',
  ('R', 'G'): '125',
  ('R', 'H'): '29',
  ('R', 'I'): '97',
  ('R', 'K'): '26',
  ('R', 'L'): '102',
  ('R', 'M'): '91',
  ('R', 'N'): '86',
  ('R', 'P'): '103',
  ('R', 'Q'): '43',
  ('R', 'R'): '0',
  ('R', 'S'): '110',
  ('R', 'T'): '71',
  ('R', 'V'): '96',
  ('R', 'W'): '101',
  ('R', 'Y'): '77',
  ('S', 'A'): '99',
  ('S', 'C'): '112',
  ('S', 'D'): '65',
  ('S', 'E'): '80',
  ('S', 'F'): '155',
  ('S', 'G'): '56',
  ('S', 'H'): '89',
  ('S', 'I'): '142',
  ('S', 'K'): '121',
  ('S', 'L'): '145',
  ('S', 'M'): '135',
  ('S', 'N'): '46',
  ('S', 'P'): '74',
  ('S', 'Q'): '68',
  ('S', 'R'): '110',
  ('S', 'S'): '0',
  ('S', 'T'): '58',
  ('S', 'V'): '124',
  ('S', 'W'): '177',
  ('S', 'Y'): '144',
  ('T', 'A'): '58',
  ('T', 'C'): '149',
  ('T', 'D'): '85',
  ('T', 'E'): '65',
  ('T', 'F'): '103',
  ('T', 'G'): '59',
  ('T', 'H'): '47',
  ('T', 'I'): '89',
  ('T', 'K'): '78',
  ('T', 'L'): '92',
  ('T', 'M'): '81',
  ('T', 'N'): '65',
  ('T', 'P'): '38',
  ('T', 'Q'): '42',
  ('T', 'R'): '71',
  ('T', 'S'): '58',
  ('T', 'T'): '0',
  ('T', 'V'): '69',
  ('T', 'W'): '128',
  ('T', 'Y'): '92',
  ('V', 'A'): '64',
  ('V', 'C'): '192',
  ('V', 'D'): '152',
  ('V', 'E'): '121',
  ('V', 'F'): '50',
  ('V', 'G'): '109',
  ('V', 'H'): '84',
  ('V', 'I'): '29',
  ('V', 'K'): '97',
  ('V', 'L'): '32',
  ('V', 'M'): '21',
  ('V', 'N'): '133',
  ('V', 'P'): '68',
  ('V', 'Q'): '96',
  ('V', 'R'): '96',
  ('V', 'S'): '124',
  ('V', 'T'): '69',
  ('V', 'V'): '0',
  ('V', 'W'): '88',
  ('V', 'Y'): '55',
  ('W', 'A'): '148',
  ('W', 'C'): '215',
  ('W', 'D'): '181',
  ('W', 'E'): '152',
  ('W', 'F'): '40',
  ('W', 'G'): '184',
  ('W', 'H'): '115',
  ('W', 'I'): '61',
  ('W', 'K'): '110',
  ('W', 'L'): '61',
  ('W', 'M'): '67',
  ('W', 'N'): '174',
  ('W', 'P'): '147',
  ('W', 'Q'): '130',
  ('W', 'R'): '101',
  ('W', 'S'): '177',
  ('W', 'T'): '128',
  ('W', 'V'): '88',
  ('W', 'W'): '0',
  ('W', 'Y'): '37',
  ('Y', 'A'): '112',
  ('Y', 'C'): '194',
  ('Y', 'D'): '160',
  ('Y', 'E'): '122',
  ('Y', 'F'): '22',
  ('Y', 'G'): '147',
  ('Y', 'H'): '83',
  ('Y', 'I'): '33',
  ('Y', 'K'): '85',
  ('Y', 'L'): '36',
  ('Y', 'M'): '36',
  ('Y', 'N'): '143',
  ('Y', 'P'): '110',
  ('Y', 'Q'): '99',
  ('Y', 'R'): '77',
  ('Y', 'S'): '144',
  ('Y', 'T'): '92',
  ('Y', 'V'): '55',
  ('Y', 'W'): '37',
  ('Y', 'Y'): '0'
}

grantham.matrix.txt should have .{tab}A in the first row instead of .{space}A