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Top Forums UNIX for Dummies Questions & Answers help! script to select line with greatest value 2 between columns Post 302566497 by wolf_blue on Thursday 20th of October 2011 12:43:30 PM
Old 10-20-2011
help! script to select line with greatest value 2 between columns

Hi,
I’m trying to do something I haven’t done before and I’m struggling with how to even create the command or script.
I have the following space delim file:

Code:
gene    accession    chr     chr_st    begin    end       
NN1        NC_024540    chr3    -    14000    14020    
NN1        NC_024543    chr3    -    14050    14060    
ATG        NC_01        chr12    +    12000    12100    
ATG        NC_02        chr12    +    12100    12300

This is an example file
I want to modify the file so that I only get the gene with the greatest length written to one file.
So want to calculate the length of each form of the genes in each row then: where length = end value- begin value

Code:
gene    accession    chr     chr_st    begin    end        length 
NN1        NC_024540    chr3    -    14000    14020    20
NN1        NC_024543    chr3    -    14050    14060    10
ATG        NC_01        chr12    +    12000    12100    100
ATG        NC_02        chr12    +    12100    12300    200

I want to be able to create a file with only the genes with greatest length which would look like this:
Code:
gene    accession    chr      chr_st    begin    end         length
NN1        NC_024540    chr3    -        14000    14020    20
ATG        NC_02        chr12    +        12100    12300    300

Any help is really aprreciated, I have 30,000 genes with different forms like this!
Thanks!

Last edited by zxmaus; 10-21-2011 at 04:41 AM.. Reason: added code tags
 

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catch(n)						       Tcl Built-In Commands							  catch(n)

__________________________________________________________________________________________________________________________________________________

NAME
catch - Evaluate script and trap exceptional returns SYNOPSIS
catch script ?varName? _________________________________________________________________ DESCRIPTION
The catch command may be used to prevent errors from aborting command interpretation. Catch calls the Tcl interpreter recursively to exe- cute script, and always returns without raising an error, regardless of any errors that might occur while executing script. If script raises an error, catch will return a non-zero integer value corresponding to one of the exceptional return codes (see tcl.h for the definitions of code values). If the varName argument is given, then the variable it names is set to the error message from interpret- ing script. If script does not raise an error, catch will return 0 (TCL_OK) and set the variable to the value returned from script. Note that catch catches all exceptions, including those generated by break and continue as well as errors. The only errors that are not caught are syntax errors found when the script is compiled. This is because the catch command only catches errors during runtime. When the catch statement is compiled, the script is compiled as well and any syntax errors will generate a Tcl error. EXAMPLES
The catch command may be used in an if to branch based on the success of a script. if { [catch {open $someFile w} fid] } { puts stderr "Could not open $someFile for writing $fid" exit 1 } The catch command will not catch compiled syntax errors. The first time proc foo is called, the body will be compiled and a Tcl error will be generated. proc foo {} { catch {expr {1 +- }} } KEYWORDS
catch, error Tcl 8.0 catch(n)
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