recoding data points using SED?? Post: 302360680

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Top Forums Shell Programming and Scripting recoding data points using SED?? Post 302360680 by doobedoo on Friday 9th of October 2009 03:56:41 PM

10-09-2009

Registered User

I apologize for the confusion! I understand where I need to go with this but I have no clue how to tell the computer to do it so it is hard for me to explain it to others as well...let me try again...

My input file currently looks like this:

ID 1 2 3 4 5 6 7 8
83845676 AG AC AT GT CC AA CC CC
83846900 AA AA TT GG CC AG CC TT
83847041 AA 00 AT GT 00 AG CG CT
83847004 AG AA TT TT CC AG CG CT
83847085 AG CC AT GT CG AG CG CT
83847118 00 AA TT GG 00 GG CC CT
83847162 GG AA TT GT CG AG CG CT
83847165 AA AA 00 GG CC AG GG CT

I want to rename the missing values so they are just a period and save an output file like this:

ID 1 2 3 4 5 6 7 8
83845676 AG AC AT GT CC AA CC CC
83846900 AA AA TT GG CC AG CC TT
83847041 AA . AT GT . AG CG CT
83847004 AG AA TT TT CC AG CG CT
83847085 AG CC AT GT CG AG CG CT
83847118 . AA TT GG . GG CC CT
83847162 GG AA TT GT CG AG CG CT
83847165 AA AA . GG CC AG GG CT

Then I need to create an output file that has all of the letters recoded as -1, 0, or 1. This should be done in alphabetical order and on a per column basis so that:

ID 1 2 3 4 5 6 7 8
83845676 0 0 0 0 -1 -1 -1 -1
83846900 -1 -1 1 -1 -1 0 -1 1
83847041 -1 . 0 0 . 0 0 0
83847004 0 -1 1 1 -1 0 0 0
83847085 0 1 0 0 0 0 0 0
83847118 . -1 1 -1 . 1 -1 0
83847162 1 -1 1 0 0 0 0 0
83847165 -1 -1 . -1 -1 0 1 0

Finally I need to calculate the average of each column and replace the missing values from that column with the average:

ID 1 2 3 4 5 6 7 8
83845676 0 0 0 0 -1 -1 -1 -1
83846900 -1 -1 1 -1 -1 0 -1 1
83847041 -1 -0.5 0 0 -0.5 0 0 0
83847004 0 -1 1 1 -1 0 0 0
83847085 0 1 0 0 0 0 0 0
83847118 -0.25 -1 1 -1 -0.5 1 -1 0
83847162 1 -1 1 0 0 0 0 0
83847165 -1 -1 0.5 -1 -1 0 1 0

This will be the final file. Does this make more since or have I confused you more??

Thanks

doobedoo

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LEARN ABOUT OSF1

temporary

Temporary(4)						     Kernel Interfaces Manual						      Temporary(4)

NAME

       Temporary - Stores data files during transfers to remote systems

SYNOPSIS

       /usr/spool/uucp/SystemName/TM.xxPID.000

DESCRIPTION

       The  uucp  Temporary  (TM.*) files store data files during transfers to remote systems.	After a Data (D.*) file is transferred to a remote
       system by the uucico daemon, the uucp program places it in a subdirectory of the uucp spooling directory named  /usr/spool/uucp/SystemName,
       where  the SystemName directory is named for the computer that is transmitting the file.  The uucp program creates a temporary data file to
       hold the original data file.

       The full pathname of the temporary data file is in the following format: /usr/spool/uucp/SystemName/TM.xxPID.000

       where the SystemName directory is named for the computer that is sending the file, and TM.xxPID.000 is the name of the file;  for  example,
       TM.00451.000.  The PID variable is the process ID of the job.

FILES

       Describes accessible remote systems Contains uucp command, data, and execute files Contain data to be transferred.  Contain files that uucp
       has transferred

RELATED INFORMATION

       Daemons: uucico(8)

       Commands: uucp(1), uudemon.cleanu(4), uupick(1), uuto(1), uux(1) delim off

																      Temporary(4)

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