CODEWITHSUNDEEP
linuxbashsorting
Chubaka
Chubaka

Reputation: 3135

linux sort $2 & $17 in numerical values, sort distant columns

If we have an input: 

cpdID,cpd_number,Cell_assay_id,Cell_alt_assay_id,Cell_type_desc,Cell_Operator,Cell_result_value,Cell_unit_value,assay_id,alt_assay_id,type_desc,operator,result_value,unit_value,Ratio_operator,Ratio,log_ratio,Cell_experiment_date,experiment_date,Cell_discipline,discipline
49,cpd-7788990,1212,2323, IC50 ,,100,uM,1334,1331,Ki,,10,uM,,10,-1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-7788990,8888,9999, IC50 ,,200,uM,1334,1331,Ki,,10,uM,,20,-3,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-7788990,5555,6666, IC50 ,>,150,uM,1334,1331,Ki,,10,uM,>,15,-2,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-6666666,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1.1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1.3,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1.2,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme

We would love to sort it as : if $2 are the same, they should be in a group. Within the same $2 group, $17 should be sorted from max to min. 

cpdID,cpd_number,Cell_assay_id,Cell_alt_assay_id,Cell_type_desc,Cell_Operator,Cell_result_value,Cell_unit_value,assay_id,alt_assay_id,type_desc,operator,result_value,unit_value,Ratio_operator,Ratio,log_ratio,Cell_experiment_date,experiment_date,Cell_discipline,discipline
49,cpd-7788990,1212,2323, IC50 ,,100,uM,1334,1331,Ki,,10,uM,,10,-1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-7788990,5555,6666, IC50 ,>,150,uM,1334,1331,Ki,,10,uM,>,15,-2,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-7788990,8888,9999, IC50 ,,200,uM,1334,1331,Ki,,10,uM,,20,-3,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-6666666,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1.1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1.2,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1.3,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme

Numbers of tries and consulting of other posts didn't seem to solve the question.

sort -nk2,17 --field-separator=',' input.csv

See $2 in cpd-1111: $17 is ordered by "-1.1, -1, -1.2, -1.3". We would like it to be -1, -1.1, -1.2, -1.3".

49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1.1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1.2,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-1111,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1.3,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-6666666,8888,9999, IC50 ,,400,uM,1334,1331,Ki,,10,uM,,40,-1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-7788990,1212,2323, IC50 ,,100,uM,1334,1331,Ki,,10,uM,,10,-1,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-7788990,5555,6666, IC50 ,>,150,uM,1334,1331,Ki,,10,uM,>,15,-2,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
49,cpd-7788990,8888,9999, IC50 ,,200,uM,1334,1331,Ki,,10,uM,,20,-3,12/6/2006 0:00,2/16/2007 0:00,Cell,Enzyme
cpdID,cpd_number,Cell_assay_id,Cell_alt_assay_id,Cell_type_desc,Cell_Operator,Cell_result_value,Cell_unit_value,assay_id,alt_assay_id,type_desc,operator,result_value,unit_value,Ratio_operator,Ratio,log_ratio,Cell_experiment_date,experiment_date,Cell_discipline,discipline

The following two don't do the trick as well. May we know if any guru might have any comment? It might be an easy one but stops us for quite a while. Thanks.

sort -rnk2,17 --field-separator=',' input.csv

sort -rnk2.17 --field-separator=',' input.csv

Upvotes: 1

Views: 323

Answers (1)

Deleted User
Deleted User

Reputation: 2541

sounds like what you want is

sort -r -t"," -k2,2 -k17,17 input.csv

Upvotes: 3

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