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Full Discussion: awk to convert table-by-row to matrix table
Top Forums Shell Programming and Scripting awk to convert table-by-row to matrix table Post 302881907 by yifangt on Thursday 2nd of January 2014 05:31:12 PM
Old 01-02-2014
additional: mark missing data with -
Thank you both!
Amazing scripts!
disedorgue, Your script is what i was thinking to use, but need more digestion.
More challenging with real data, that some members (i.e. columns) of some site are with missing data as indicated with "-" in previous post, but not listed in the infile, which will be assigned with an empty cell and will cause confusion.
Code:
infile: 
site1 A:o,p,q,r,s,t
site1 C:y,u
site1 T:v,w
site1 -:x,z
site2 A:p,r,t,v,w,z
site2 C:u,y
site2 G:q,s
site3 A:o,q,s,t,u,z
site3 C:y
site3 T:v,w,x

Code:
output:
SITE    o p q r s t u v w x y z 
site1    A A A A A A C T T - C - 
site2     A G A G A C A A  C A 
site3    A  A  A A A T T T C A

How to add "-" to those "empty" cells so that the table is aligned? Thanks a lot again!
Last edited by yifangt; 01-02-2014 at 06:35 PM.. Reason: typo
 

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