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Full Discussion: CSv2dat file headers and columns order
Top Forums Shell Programming and Scripting CSv2dat file headers and columns order Post 302898447 by grikoss on Tuesday 22nd of April 2014 08:58:32 AM
Old 04-22-2014
CSv2dat file headers and columns order
Dear all,

I have a csv file which is transformed to .dat. I have an awk file which is supposing to do the mapping of the dat file. the code from the awk file is the one below.

The content of the dat file is looking like this (tab separated):
Code:
ODT   AGE        CDT    CO    SEX    TIME    VALUE    COMMENT
P3      Y6-8         ACT    FG    F         2011       1297        
P4      Y3-4         EMP    FG    M        2011       6940           b
P1      Y7-9         GRT    FG    F          2011       0                 c

what I have to do is the following:
1. keep the headers together with the columns order - done
2. if the value for COMMENT is "c" then the column COMMENT must be changed to STRING_COM, if the value for COMMENT is "b" (or anything different than "c") the COMMENT column must be changed to STRING_STATUS
3. No matter what other columns will be received except the ones mentioned here they must be removed
4. VALUE column should be renamed in "NUMB"

Here is my code which fix only the 1st point
Code:
BEGIN { 
  FS = "," ;
  OFS = "    " ;  
}

{ 

if(NR == 1)
{
  split($0, tmp, ",");
  for(i = 1; i <= NF; i++) 
  fields[tmp[i]] = i
  print tmp[1], tmp[2], tmp[3], tmp[4], tmp[5], tmp[6], tmp[7], tmp[8]

else
{
  split($0, tmp, ",");
  for(i = 1; i <= NF; i++) 
  fields[tmp[i]] = i

  print tmp[1], tmp[2], tmp[3], tmp[4], tmp[5], tmp[6], tmp[7], tmp[8]
}
}

expected result in the dat file:
Code:
ODT   AGE        CDT    CO    SEX    TIME    NUMB STRING_COM STRING_STATUS
P3      Y6-8         ACT    FG    F         2011       1297        
P4      Y3-4         ERT    FG    M        2011       6940           b
P1      Y7-9         GRT    FG    F          2011       0                           c

Thank you in advance
Last edited by Franklin52; 04-23-2014 at 02:59 AM.. Reason: Please use code tags
 

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LEARN ABOUT SUNOS

unknown

UNKNOWN(1)						      General Commands Manual							UNKNOWN(1)

NAME

       unknown - identify possible genotypes for unknowns

SYNOPSIS

       A program to rapidly identify which genotypes are possible for individuals typed as unknowns in the input pedigree.

       unknown [ -cl ]

DESCRIPTION

       unknown infers possible genotypes and mating combinations for parents with unknown genotypes for ilink(1), mlink(1) and linkmap(1).

OPTIONS

       -c     Use conditional allele frequencies.

       -l     Choose a good set of loop breakers automatically.

RETURN VALUE

       0     Successful completion

ERRORS

       10    File not found
       255   Failure

EXAMPLES

       Normally, unknown(1) is run immediately prior to its sister programs, ilink(1), mlink(1) and linkmap(1), like this:

       unknown
       mlink

FILES

       unknown(1) reads the two files pedfile.dat and datafile.dat as its own input and produces various temporary files that are used as input to
       the next program. These temporary files are ipedfile.dat, upedfile.dat, speedfile.dat and newspeedfile.dat.

NOTES

       unknown(1) is part of the FASTLINK package, which is a re-implementation of the LINKAGE suite  of  computer  tools  that  help  investigate
       genetic linkage as first proposed G.M. Lathrop, J.M. Lalouel, C. Julier, and J. Ott.

AUTHORS

       Dylan Cooper, Alejandro Schaffer, and Tony Schurtz based on work originally by Jurg Ott, Ph.D, et. al.

       This manual page was written by Elizabeth Barham <lizzy@soggytrousers.net> for the Debian GNU/Linux system (but may be used by others).

WORD-WIDE-WEB
       http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html

SEE ALSO

       ilink(1), linkmap(1), lodscore(1), mlink(1).

								  April 15, 2003							UNKNOWN(1)
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