; convert-matrix  -v 1 -i data/yeast_study_case/prodoric/FNR_bacillus/FNR_bacillus.infogibbs -from infogibbs -to tab -o /Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_matrix_info.txt -bgfile /Users/amedina/local/rsa-tools/data/genomes/Bacillus_subtilis/oligo-frequencies/2nt_upstream-noorf_Bacillus_subtilis-ovlp-2str.freq.gz -bg_format oligos -return counts,frequencies,weights,info,parameters,sites,logo -logo_format png,pdf -logo_opt '-e -M -t FNR_bacillus ' -logo_file /Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo
; Input files
;	input	data/yeast_study_case/prodoric/FNR_bacillus/FNR_bacillus.infogibbs
;	prior	/Users/amedina/local/rsa-tools/data/genomes/Bacillus_subtilis/oligo-frequencies/2nt_upstream-noorf_Bacillus_subtilis-ovlp-2str.freq.gz
; Input format        	infogibbs
; Output files
;	output	/Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_matrix_info.txt
; Output format       	tab
; pseudo-weight       	1
; Background model
;	Strand        	insensitive
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.32071
;		c	0.17947
;		g	0.17897
;		t	0.32085
a	|	1	0	0	0	7	5	5	0	5	1	2	0	0	7	0	6
c	|	0	0	0	0	0	1	0	1	0	3	0	0	7	0	7	0
g	|	0	7	0	7	0	0	2	0	1	1	0	1	0	0	0	0
t	|	6	0	7	0	0	1	0	6	1	2	5	6	0	0	0	1
//
a	|  0.2  0.0  0.0  0.0  0.9  0.7  0.7  0.0  0.7  0.2  0.3  0.0  0.0  0.9  0.0  0.8
c	|  0.0  0.0  0.0  0.0  0.0  0.1  0.0  0.1  0.0  0.4  0.0  0.0  0.9  0.0  0.9  0.0
g	|  0.0  0.9  0.0  0.9  0.0  0.0  0.3  0.0  0.1  0.1  0.0  0.1  0.0  0.0  0.0  0.0
t	|  0.8  0.0  0.9  0.0  0.0  0.2  0.0  0.8  0.2  0.3  0.7  0.8  0.0  0.0  0.0  0.2
//
a	| -0.7 -2.1 -2.1 -2.1  1.0  0.7  0.7 -2.1  0.7 -0.7 -0.1 -2.1 -2.1  1.0 -2.1  0.9
c	| -2.1 -2.1 -2.1 -2.1 -2.1 -0.2 -2.1 -0.2 -2.1  0.8 -2.1 -2.1  1.6 -2.1  1.6 -2.1
g	| -2.1  1.6 -2.1  1.6 -2.1 -2.1  0.4 -2.1 -0.2 -0.2 -2.1 -0.2 -2.1 -2.1 -2.1 -2.1
t	|  0.9 -2.1  1.0 -2.1 -2.1 -0.7 -2.1  0.9 -0.7 -0.1  0.7  0.9 -2.1 -2.1 -2.1 -0.7
//
a	| -0.1 -0.1 -0.1 -0.1  1.0  0.5  0.5 -0.1  0.5 -0.1 -0.0 -0.1 -0.1  1.0 -0.1  0.7
c	| -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0  0.3 -0.0 -0.0  1.4 -0.0  1.4 -0.0
g	| -0.0  1.4 -0.0  1.4 -0.0 -0.0  0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0
t	|  0.7 -0.1  1.0 -0.1 -0.1 -0.1 -0.1  0.7 -0.1 -0.0  0.5  0.7 -0.1 -0.1 -0.1 -0.1
//
; Sites	7
>1
TGTGACATAGTTCACA
>2
TGTGAAATACATCACT
>3
TGTGATGTAATTCACA
>4
TGTGAAATACTTCACA
>5
TGTGAAGTGTTGCACA
>6
TGTGAAATACTTCACA
>7
AGTGAAACTTATCACA
;
; Matrix parameters
;	Columns                      	16
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.320705545565842|c:0.179472076806283|g:0.178972760582602|t:0.320849617045273
;	program                      	infogibbs
;	matrix.nb                    	1
;	sites                        	7
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.178973
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	10.9832
;	information.per.column       	0.686453
;	max.possible.info.per.col    	1.72052
;	consensus.strict             	tGTGAaatacttCACa
;	consensus.strict.rc          	TGTGAAGTATTTCACA
;	consensus.IUPAC              	tGTGAartacttCACa
;	consensus.IUPAC.rc           	TGTGAAGTAYTTCACA
;	consensus.regexp             	tGTGAa[ag]tacttCACa
;	consensus.regexp.rc          	TGTGAAGTA[CT]TTCACA
;	residues.content.crude.freq  	a:0.3482|c:0.1696|g:0.1696|t:0.3125
;	G+C.content.crude.freq       	0.339286
;	residues.content.corrected.freq	a:0.3448|c:0.1709|g:0.1708|t:0.3135
;	G+C.content.corrected.freq   	0.341681
;	min(P(S|M))                  	2.62977e-26
;	max(P(S|M))                  	0.0150617
;	proba_range                  	0.0150617
;	Wmin                         	-32
;	Wmax                         	17
;	Wrange                       	49
; logo file:/Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo_m1.png
; logo file:/Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo_m1.pdf
; logo file:/Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo_m1_rc.png
; logo file:/Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo_m1_rc.pdf
; Job started 2010_03_26.124243
; Job done    2010_03_26.124255