Fixing a shell script Post: 302957318

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Top Forums Shell Programming and Scripting Fixing a shell script Post 302957318 by RudiC on Friday 9th of October 2015 06:35:20 AM

10-09-2015

Registered User

This one creates three files: DNA.OUT, RNA.OUT, and AminoAcids from the input file, and prints the numbers of non-empty and empty lines in the file:

Code:

awk '
/^[     ]*$/    {EMP++
                 next
                }
/^>/    {$0=""
        }

        {print > "DNA.out"
         gsub (/A/, "U")
         gsub (/C/, "c")
         gsub (/G/, "C")
         gsub (/T/, "A")
         gsub (/c/, "G")
         print > "RNA.OUT"
         gsub (/.../, "& ")
         gsub (/UU[CU] /, "Phe ")
         gsub (/UA[UC] /, "Tyr ")
         gsub (/GC[ACGU] /, "Ala ")
         gsub (/GG[ACGU] /, "Gly ")
         gsub (/CC[ACGU] /, "Pro ")
         gsub (/AC[ACGU] /, "Thr ")
         gsub (/GU[ACGU] /, "Val ")
         gsub (/(CG[ACGU]|AG[AG]) /, "Arg ")
         gsub (/(CU[ACGU]|UU[AG]) /, "Leu ")
         gsub (/(UC[ACGU]|AG[CU]) /, "Ser ")
         print > "AminoAcids"
        }

END     {print "lines: ", NR-EMP
         print "empty: ", EMP
        }
' file

I did NOT convert ALL of the RNA-Amino combinations from your sed file; should be easliy doable for you with the samples given...

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yri

YRI(1)																	    YRI(1)

NAME

       yri - documentation tool in console for Ruby

SYNOPSIS

       yri [options] Path_to_object

DESCRIPTION

       yard(1) is an extensible documentation generation tool for the Ruby programming language. It enables the user to generate consistent,
       usable documentation that can be exported to a number of formats very easily, and also supports extending for custom Ruby constructs such
       as custom class level definitions.

       yri(1), synonym for yard ri gives the possibility to read the documentation for Ruby programs inside a console, pretty much like ri(1).

OPTIONS

   General Options:
       -b, --db FILE
	   Use a specified .yardoc db to search in

       -T, --no-pager
	   No pager

       -p, --pager PAGER
	   Use PAGER as a pager

   Other options:
       -e, --load FILE
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       --plugin PLUGIN
	   Load a YARD plugin (gem with `yard-' prefix)

       --legacy
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       --safe
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EXAMPLES

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SEE ALSO

       yard(1).

AUTHORS

       yard has been developed by Loren Segal <lsegal@soen.ca>.

       This manual page has been written for the Debian Project by CA(C)dric Boutillier (but may used by others).

								    2012-05-08								    YRI(1)