Genetic Sequence Binary Factor Grouping 


	(EXAMPLE routine order) 

(1) Number Series scale file creation 

	b16d_41 MG1999052809AA.CEL


(2) Sequence Grouping Routines 

	(single CEL file operations)

	mm30315d xd.txt MG1999052809AA.CEL > a_all.txt

	i2a13  a_all.txt 0,25,  > "_000-025.txt"
	i2a13  a_all.txt 0,50,  > "_026-050.txt"
	i2a13  a_all.txt 0,75,  > "_051-075.txt"
	i2a13  a_all.txt 0,100, > "_076-100.txt"
	i2a13  a_all.txt 0,125, > "_101-125.txt"
	i2a13  a_all.txt 0,150, > "_126-150.txt"
	i2a13  a_all.txt 0,175, > "_151-175.txt"
	i2a13  a_all.txt 0,200, > "_176-200.txt"
	i2a13  a_all.txt 0,225, > "_201-225.txt"
	i2a13  a_all.txt 0,250, > "_226-250.txt"
	i2a13  a_all.txt 0,275, > "_251-275.txt"
	i2a13  a_all.txt 0,300, > "_276-300.txt"
	i2a13  a_all.txt 0,325, > "_301-325.txt"
	i2a13  a_all.txt 0,350, > "_326-350.txt"
	i2a13  a_all.txt 0,375, > "_351-375.txt"
	i2a13  a_all.txt 0,400, > "_376-400.txt"
	i2a13  a_all.txt 0,425, > "_401-425.txt"
	i2a13  a_all.txt 0,450, > "_426-450.txt"
	i2a13  a_all.txt 0,475, > "_451-475.txt"
	i2a13  a_all.txt 0,500, > "_476-500.txt"
	i2a13  a_all.txt 0,525, > "_501-525.txt"
	i2a13  a_all.txt 0,550, > "_526-550.txt"

	a13  "_000-025.txt" > a13_1.txt
	a13  "_026-050.txt" > a13_2.txt
	a13  "_051-075.txt" > a13_3.txt
	a13  "_076-100.txt" > a13_4.txt
	a13  "_101-125.txt" > a13_5.txt
	a13  "_126-150.txt" > a13_6.txt
	a13  "_151-175.txt" > a13_7.txt
	a13  "_176-200.txt" > a13_8.txt
	a13  "_201-225.txt" > a13_9.txt
	a13  "_226-250.txt" > a13_10.txt
	a13  "_251-275.txt" > a13_11.txt
	a13  "_276-300.txt" > a13_12.txt
	a13  "_301-325.txt" > a13_13.txt
	a13  "_326-350.txt" > a13_14.txt
	a13  "_351-375.txt" > a13_15.txt
	a13  "_376-400.txt" > a13_16.txt
	a13  "_401-425.txt" > a13_17.txt
	a13  "_426-450.txt" > a13_18.txt
	a13  "_451-475.txt" > a13_19.txt
	a13  "_476-500.txt" > a13_20.txt
	a13  "_501-525.txt" > a13_21.txt
	a13  "_526-550.txt" > a13_22.txt

	copy a13_1.txt+a13_2.txt+a13_3.txt+a13_4.txt+a13_5.txt+a13_6.txt+
	a13_7.txt+a13_8.txt+a13_9.txt+a13_10.txt+a13_11.txt+a13_12.txt+
	a13_13.txt+a13_14.txt+a13_15.txt+a13_16.txt+a13_17.txt+
	a13_18.txt+a13_19.txt+a13_20.txt+a13_21.txt+a13_22.txt a13.txt

	a123all.exe
	copy r13_all.txt a.txt
	mm300 > a.bat
	ims > b.txt

	(all CEL folders results copy)

	copy E:\ALL_scans_1_\gm_1\b.txt 	E:\ALL_scans_1_\_1
	copy E:\ALL_scans_1_\gm_2\b.txt 	E:\ALL_scans_1_\_2
	copy E:\ALL_scans_1_\gm_3\b.txt 	E:\ALL_scans_1_\_3
	copy E:\ALL_scans_1_\gm_4\b.txt 	E:\ALL_scans_1_\_4
	copy E:\ALL_scans_1_\gm_5\b.txt 	E:\ALL_scans_1_\_5
	copy E:\ALL_scans_1_\gm_6\b.txt 	E:\ALL_scans_1_\_6
	copy E:\ALL_scans_1_\gm_7\b.txt 	E:\ALL_scans_1_\_7
	copy E:\ALL_scans_1_\gm_8\b.txt 	E:\ALL_scans_1_\_8
	copy E:\ALL_scans_1_\gm_9\b.txt 	E:\ALL_scans_1_\_9
	copy E:\ALL_scans_1_\gm_a10\b.txt 	E:\ALL_scans_1_\_a10

(3) Marked sequence index files creation (all CEL folders)

	cd ./_1
	a2_t
	ls > ls.txt

	cd ../_2
	a2_t
	ls > ls.txt	

	cd ../_3
	a2_t
	ls > ls.txt

	cd ../_4
	a2_t
	ls > ls.txt

	cd ../_5
	a2_t
	ls > ls.txt

	cd ../_6
	a2_t
	ls > ls.txt

	cd ../_7
	a2_t
	ls > ls.txt

	cd ../_8
	a2_t
	ls > ls.txt

	cd ../_9
	a2_t
	ls > ls.txt
	cd ../_a10
	a2_t
	ls > ls.txt

	cd ..
	cd ..

(4) Catalog file creation (all CEL folders into single file)

	cs_2x12_1.cpp > catalogue.txt 


(5) Catalog permutation group (eg elements EFG)

	(catalog segment eg !EFG contents in lc_seg_EFG.txt)
	seg_22.cpp > res_lc_seg_EFG.txt


(6) Probe 1 permutations (eg elements EFG) into permutation groups

	(all probe 1 permutations in probe_1_perm.txt)

	(3 elements permutations)
	per_1x3.cpp > res_probe_1_perm.txt

	(4 elements permutations)
	per_1x4.cpp > res_probe_1_perm.txt


(7) Single permutation group (eg lc_perm_E1F4G1.txt) into CEL reference chart
	(requires eg tumor_1_all.txt contatining all probe 1 chart data from res_lc_seg_EFG.txt)

	per_2.cpp > res_lc_perm_E1F4G1.txt

	- referenced index files chart creation 


(8) Referenced genes file creation

	(all CEL folders results copy)


	copy F:\lung_scans_16_\11c_15\gm_7\xd.txt F:\lc_E1F4G1\_5_7
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_8\xd.txt F:\lc_E1F4G1\_5_8
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_9\xd.txt F:\lc_E1F4G1\_5_9
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a10\xd.txt F:\lc_E1F4G1\_5_a10
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a11\xd.txt F:\lc_E1F4G1\_5_a11
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a12\xd.txt F:\lc_E1F4G1\_5_a12
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a13\xd.txt F:\lc_E1F4G1\_5_a13
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a14\xd.txt F:\lc_E1F4G1\_5_a14
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a15\xd.txt F:\lc_E1F4G1\_5_a15
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a16\xd.txt F:\lc_E1F4G1\_5_a16
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a17\xd.txt F:\lc_E1F4G1\_5_a17
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a18\xd.txt F:\lc_E1F4G1\_5_a18
	ts_ce_33.cpp > res_xd.txt

	copy F:\lung_scans_16_\11c_15\gm_a19\xd.txt F:\lc_E1F4G1\_5_a19
	ts_ce_33.cpp > res_xd.txt


	copy F:\lc_E1F4G1\_5_1\res_xd.txt+F:\lc_E1F4G1\_5_2\res_xd.txt+F:\lc_E1F4G1\_5_3\res_xd.txt+
	F:\lc_E1F4G1\_5_4\res_xd.txt+F:\lc_E1F4G1\_5_5\res_xd.txt a.txt

	(input a.txt)
	ts_41.cpp > res_all_1.txt

	(input res_all_1.txt and all folders xd.txt for a given index range)	
	ts_42.cpp > res_all_2.txt

	(sort res_all_2.txt into eg res_all_3.txt by column B)
	ts_44.cpp > chart_probe_res.txt


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and can be used, copied, sold, redistributed or used in any other way only by written permission of Jasenko Dzinleski . 
Copyright (C) from 2001 - 2010 and later by Jasenko Dzinleski

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if not opposite to (1) .
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