GAAIN

Como parte del proyecto GAAIN hay una parte de los datos que publicamos a trves de este consorcio. El formato de salida que me da Sergi es raro asi que voy a convertirlo

segun la leyenda esta

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case=> Subject ID
born_date=> Date
sex=> 1=Male, 2=Female 
age_diag_bassal=> Years
race_ethnic=> 0=Unknown, 1=White, 2=Southamerica, 3=Black, 4=Northafrica, 5=Gypsy, 6=Asia
AF_Demencia_A=> 0="no parent affected", 1="Father/Mother affected", 3=Unknown
APOE=> 0=unknown, 1=e2e2, 2=e2e3, 3=e2e4, 4=e3e3, 5=e3e4, 6=e4e4
dateNeuropsyc.1=> date neuropsychological assessment 1
dateNeuropsyc.2=> date neuropsychological assessment 2
dateNeuropsyc.3=> date neuropsychological assessment 3
dateNeuropsyc.4=> date neuropsychological assessment 4
dateNeuropsyc.5=> date neuropsychological assessment 5
dateNeuropsyc.6=> date neuropsychological assessment 6
dateNeuropsyc.7=> date neuropsychological assessment 7
dateNeuropsyc.8=> date neuropsychological assessment 8
dateNeuropsyc.9=> date neuropsychological assessment 9
dateNeuropsyc.10=> date neuropsychological assessment 10
dateNeuropsyc.11=> date neuropsychological assessment 11
dateNeuropsyc.12=> date neuropsychological assessment 12
M_RECOG_NP.1=> recognition score wms-III neuropsychological assessment 1
M_RECOG_NP.2=> recognition score wms-III neuropsychological assessment 2
M_RECOG_NP.3=> recognition score wms-III neuropsychological assessment 3
M_RECOG_NP.4=> recognition score wms-III neuropsychological assessment 4
M_RECOG_NP.5=> recognition score wms-III neuropsychological assessment 5
M_RECOG_NP.6=> recognition score wms-III neuropsychological assessment 6
M_RECOG_NP.7=> recognition score wms-III neuropsychological assessment 7
M_RECOG_NP.8=> recognition score wms-III neuropsychological assessment 8
M_RECOG_NP.9=> recognition score wms-III neuropsychological assessment 9
M_RECOG_NP.10=> recognition score wms-III neuropsychological assessment 10
M_RECOG_NP.11=> recognition score wms-III neuropsychological assessment 11
M_RECOG_NP.12=> recognition score wms-III neuropsychological assessment 12
M_RETENC_NP.1=> retention score wms-III neuropsychological assessment 1
M_RETENC_NP.2=> retention score wms-III neuropsychological assessment 2
M_RETENC_NP.3=> retention score wms-III neuropsychological assessment 3
M_RETENC_NP.4=> retention score wms-III neuropsychological assessment 4
M_RETENC_NP.5=> retention score wms-III neuropsychological assessment 5
M_RETENC_NP.6=> retention score wms-III neuropsychological assessment 6
M_RETENC_NP.7=> retention score wms-III neuropsychological assessment 7
M_RETENC_NP.8=> retention score wms-III neuropsychological assessment 8
M_RETENC_NP.9=> retention score wms-III neuropsychological assessment 9
M_RETENC_NP.10=> retention score wms-III neuropsychological assessment 10
M_RETENC_NP.11=> retention score wms-III neuropsychological assessment 11
M_RETENC_NP.12=> retention score wms-III neuropsychological assessment 12
date_followup.0=> Date neurological exploration 0 (basal diagnose)
date_followup.1=> Date neurological exploration 1 (followup)
date_followup.2=> Date neurological exploration 2 (followup)
date_followup.3=> Date neurological exploration 3 (followup)
date_followup.4=> Date neurological exploration 4 (followup)
date_followup.5=> Date neurological exploration 5 (followup)
date_followup.6=> Date neurological exploration 6 (followup)
date_followup.7=> Date neurological exploration 7 (followup)
date_followup.8=> Date neurological exploration 8 (followup)
date_followup.9=> Date neurological exploration 9 (followup)
date_followup.10=> Date neurological exploration 10 (followup)
date_followup.11=> Date neurological exploration 11 (followup)
date_followup.12=> Date neurological exploration 12 (followup)
date_followup.13=> Date neurological exploration 13 (followup)
date_followup.14=> Date neurological exploration 14 (followup)
date_followup.15=> Date neurological exploration 15 (followup)
date_followup.16=> Date neurological exploration 16 (followup)
date_followup.17=> Date neurological exploration 17 (followup)
date_followup.18=> Date neurological exploration 18 (followup)
date_followup.19=> Date neurological exploration 19 (followup)
cdr_followup.0=> cdr neurological exploration 0 (basal diagnose)
cdr_followup.1=> cdr neurological exploration 1 (followup)
cdr_followup.2=> cdr neurological exploration 2 (followup)
cdr_followup.3=> cdr neurological exploration 3 (followup)
cdr_followup.4=> cdr neurological exploration 4 (followup)
cdr_followup.5=> cdr neurological exploration 5 (followup)
cdr_followup.6=> cdr neurological exploration 6 (followup)
cdr_followup.7=> cdr neurological exploration 7 (followup)
cdr_followup.8=> cdr neurological exploration 8 (followup)
cdr_followup.9=> cdr neurological exploration 9 (followup)
cdr_followup.10=> cdr neurological exploration 10 (followup)
cdr_followup.11=> cdr neurological exploration 11 (followup)
cdr_followup.12=> cdr neurological exploration 12 (followup)
cdr_followup.13=> cdr neurological exploration 13 (followup)
cdr_followup.14=> cdr neurological exploration 14 (followup)
cdr_followup.15=> cdr neurological exploration 15 (followup)
cdr_followup.16=> cdr neurological exploration 16 (followup)
cdr_followup.17=> cdr neurological exploration 17 (followup)
cdr_followup.18=> cdr neurological exploration 18 (followup)
cdr_followup.19=> cdr neurological exploration 19 (followup)
mmse_followup.0=> mmse neurological exploration 0 (basal diagnose)
mmse_followup.1=> mmse neurological exploration 1 (followup)
mmse_followup.2=> mmse neurological exploration 2 (followup)
mmse_followup.3=> mmse neurological exploration 3 (followup)
mmse_followup.4=> mmse neurological exploration 4 (followup)
mmse_followup.5=> mmse neurological exploration 5 (followup)
mmse_followup.6=> mmse neurological exploration 6 (followup)
mmse_followup.7=> mmse neurological exploration 7 (followup)
mmse_followup.8=> mmse neurological exploration 8 (followup)
mmse_followup.9=> mmse neurological exploration 9 (followup)
mmse_followup.10=> mmse neurological exploration 10 (followup)
mmse_followup.11=> mmse neurological exploration 11 (followup)
mmse_followup.12=> mmse neurological exploration 12 (followup)
mmse_followup.13=> mmse neurological exploration 13 (followup)
mmse_followup.14=> mmse neurological exploration 14 (followup)
mmse_followup.15=> mmse neurological exploration 15 (followup)
mmse_followup.16=> mmse neurological exploration 16 (followup)
mmse_followup.17=> mmse neurological exploration 17 (followup)
mmse_followup.18=> mmse neurological exploration 18 (followup)
mmse_followup.19=> mmse neurological exploration 19 (followup)
diag_followup.0=> diagnose neurological exploration 0 (basal diagnose). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.1=> diagnose neurological exploration 1 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.2=> diagnose neurological exploration 2 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.3=> diagnose neurological exploration 3 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.4=> diagnose neurological exploration 4 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.5=> diagnose neurological exploration 5 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.6=> diagnose neurological exploration 6 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.7=> diagnose neurological exploration 7 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.8=> diagnose neurological exploration 8 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.9=> diagnose neurological exploration 9 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.10=> diagnose neurological exploration 10 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.11=> diagnose neurological exploration 11 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.12=> diagnose neurological exploration 12 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.13=> diagnose neurological exploration 13 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.14=> diagnose neurological exploration 14 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.15=> diagnose neurological exploration 15 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.16=> diagnose neurological exploration 16 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.17=> diagnose neurological exploration 17 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.18=> diagnose neurological exploration 18 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others
diag_followup.19=> diagnose neurological exploration 19 (followup). 1=Control, 2=Others, 3=MCI, 4=AD, 5=Others

El formato de partida es una cosa asi:

case;born_date;sex;age_diag_bassal;race_ethnic;AF_Demencia_A;APOE;dateNeuropsyc.1;dateNeuropsyc.2;dateNeuropsyc.3;dateNeuropsyc.4;dateNeuropsyc.5;dateNeuropsyc.6;dateNeuropsyc.7;dateNeuropsyc.8;dateNeuropsyc.9;dateNeuropsyc.10;dateNeuropsyc.11;dateNeuropsyc.12;M_RECOG_NP.1;M_RECOG_NP.2;M_RECOG_NP.3;M_RECOG_NP.4;M_RECOG_NP.5;M_RECOG_NP.6;M_RECOG_NP.7;M_RECOG_NP.8;M_RECOG_NP.9;M_RECOG_NP.10;M_RECOG_NP.11;M_RECOG_NP.12;M_RETENC_NP.1;M_RETENC_NP.2;M_RETENC_NP.3;M_RETENC_NP.4;M_RETENC_NP.5;M_RETENC_NP.6;M_RETENC_NP.7;M_RETENC_NP.8;M_RETENC_NP.9;M_RETENC_NP.10;M_RETENC_NP.11;M_RETENC_NP.12;date_followup.0;date_followup.1;date_followup.2;date_followup.3;date_followup.4;date_followup.5;date_followup.6;date_followup.7;date_followup.8;date_followup.9;date_followup.10;date_followup.11;date_followup.12;date_followup.13;date_followup.14;date_followup.15;date_followup.16;date_followup.17;date_followup.18;date_followup.19;cdr_followup.0;cdr_followup.1;cdr_followup.2;cdr_followup.3;cdr_followup.4;cdr_followup.5;cdr_followup.6;cdr_followup.7;cdr_followup.8;cdr_followup.9;cdr_followup.10;cdr_followup.11;cdr_followup.12;cdr_followup.13;cdr_followup.14;cdr_followup.15;cdr_followup.16;cdr_followup.17;cdr_followup.18;cdr_followup.19;mmse_followup.0;mmse_followup.1;mmse_followup.2;mmse_followup.3;mmse_followup.4;mmse_followup.5;mmse_followup.6;mmse_followup.7;mmse_followup.8;mmse_followup.9;mmse_followup.10;mmse_followup.11;mmse_followup.12;mmse_followup.13;mmse_followup.14;mmse_followup.15;mmse_followup.16;mmse_followup.17;mmse_followup.18;mmse_followup.19;diag_followup.0;diag_followup.1;diag_followup.2;diag_followup.3;diag_followup.4;diag_followup.5;diag_followup.6;diag_followup.7;diag_followup.8;diag_followup.9;diag_followup.10;diag_followup.11;diag_followup.12;diag_followup.13;diag_followup.14;diag_followup.15;diag_followup.16;diag_followup.17;diag_followup.18;diag_followup.19
4556;1931-01-10;2;74,4;0;0;;2005-05-13;2006-02-24;;;;;;;;;;;;2;;;;;;;;;;;;0;;;;;;;;;;;2005-05-24;2006-02-24;2006-12-01;2007-06-15;2008-01-24;2008-10-09;2009-05-11;2009-11-09;2010-03-29;2010-12-20;2011-06-27;2012-01-09;2012-04-11;2012-06-27;2012-09-19;2012-11-07;2013-05-06;2014-03-06;2014-11-17;;;1;1;2;2;;2;2;3;3;3;3;3;3;3;3;3;3;3;;18;17;18;15;16;16;16;14;12;8;9;6;1;1;1;1;;1;;;4;4;4;4;4;4;4;4;4;4;4;4;4;4;4;4;4;4;4;

Asi que primero convierto las comas en puntos, los punto y coma en comas y despues me fajo con los APOE.

$ sed 's/,/./g' gaain_oscar2.csv | sed 's/;/,/g' > tmp_gaain.csv

y ahora vamos a cambiar el APOE

$ sed 's/e2e2/1/;s/e2e3/2/;s/e2e4/3/;s/e3e3/4/;s/e3e4/5/;s/e4e4/6/' tmp_gaain.csv > gaain_matrix_try.csv

y ahora compruebo que tal van los APOE:

$  awk -F "," '{if(!$7) print}' gaain_matrix_try.csv | wc -l
9071
$  awk -F "," '{if($7==0) print}' gaain_matrix_try.csv | wc -l
0
$  awk -F "," '{if($7==1) print}' gaain_matrix_try.csv | wc -l
4
$  awk -F "," '{if($7==2) print}' gaain_matrix_try.csv | wc -l
150
$  awk -F "," '{if($7==3) print}' gaain_matrix_try.csv | wc -l
53
$  awk -F "," '{if($7==4) print}' gaain_matrix_try.csv | wc -l
1683
$  awk -F "," '{if($7==5) print}' gaain_matrix_try.csv | wc -l
1016
$  awk -F "," '{if($7==6) print}' gaain_matrix_try.csv | wc -l
167