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Full Discussion: Help with processing coordinates in a file.
Top Forums UNIX for Beginners Questions & Answers Help with processing coordinates in a file. Post 303030112 by RudiC on Wednesday 6th of February 2019 05:58:44 AM
Old 02-06-2019
Please explain how this line
Code:
Solyc00g005060.1.1    SL3.0ch02    702679    C    A    -    -    -    -    -    -    -    -

made it into the desired ouput - there is no connection between Solyc00g005060.1.1 and SL3.0ch02 in your annotation file, but it exists for the Solyc00g005000.3.1 and SL3.0ch02 pair. And, why isn't Solyc00g005050.3.1 / SL3.0ch00 mentioned? Shouldn't that match the third variation line?


Howsoever, pls try and report back
Code:
awk '
NR==FNR         {a[$2 FS $3 FS $4] = $1
                 next
                }
                {for (i in a) if (split (i,t) && $2>=t[2] && $2<=t[3])  print a[i], $0
                }
' annotation.txt variation.txt
Solyc00g005000.3.1 SL3.0ch02     702679    C     A     -     -     -     -     -     -     -     -    
Solyc00g005040.3.1 SL3.0ch00     715124    G     A     -     -     -     -     -     -     -     -
Solyc00g005060.1.1 SL3.0ch00     723860    A     C     Solyc00g005060.1     CDS     NONSYNONYMOUS     W/G     52    0    novel     DELETERIOUS (*WARNING! Low confidence)
Solyc00g005080.2.1 SL3.0ch00     723860    A     C     Solyc00g005060.1     CDS     NONSYNONYMOUS     W/G     52    0    novel     DELETERIOUS (*WARNING! Low confidence)
Solyc00g005060.1.1 SL3.0ch00     723867    A     C     Solyc00g005060.1     CDS     SYNONYMOUS     G/G     49    1    novel     TOLERATED
Solyc00g005080.2.1 SL3.0ch00     723867    A     C     Solyc00g005060.1     CDS     SYNONYMOUS     G/G     49    1    novel     TOLERATED
Solyc00g005060.1.1 SL3.0ch00     723903    T     C     Solyc00g005060.1     CDS     SYNONYMOUS     G/G     37    1    novel     TOLERATED

Its results match the desired output except for the two mentioned lines plus, mayhap, the field separators (which weren't specified, btw).
 

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LEARN ABOUT DEBIAN

grcompiler

grcompiler(1)															     grcompiler(1)

NAME

       grcompiler - Compile GDL into a TrueType Font

SYNOPSIS

       grcompiler [-d] [-D] [-g] [-n number] [-v number] [-w number] [-wall] [-q] gdl-file font-file [output-file] [output-fontname]

Description
       Grcompiler  compiles  a	Graphite Description Language description of the smarts for a font along with a TrueType Font to create a graphite
       font with graphite tables in it.

       -d     Generate XML debugger file.

       -D     Generate all debugger files.

       -g     Permit and ignore invalid glyph definitions.

       -nnumber
	      Set name table start location.

       -q     Quiet mode (no messages except on error).

       -vnumber
	      Set Silf table version number.

       -wnnnn Ignore warning with the given number. This option may be repeated.

       -wall  Display all warnings.

Environment
       grcompiler makes use of the following environment variables

       GDLPP  Specifies the command to execute to run the GDL preprocessor

Files
       gdlerr.txt
	      Warnings and errors are output to this file.

       dbg_classes.txt
	      Debug file that specifies the classes stored in the font in terms of their GDL source and containing glyph ids in hex.

       dbg_cmap.txt
	      Debug file giving Unicode to glyph mapping of all the glyphs in the font and vice versa.

       dbg_enginecode.txt
	      Debug file containing the action code and constraint code associated with each pass and rule in a pass.

       dbg_fsm.txt
	      Debug file that gives the finite state machines of each pass and the rules referenced. For each pass, a  mapping	is  given  between
	      glyph and column number.

       dbg_glyphattrs.txt
	      Debug file containing all the glyph attributes and their names, along with values specified for each glyph.

       dbg_parsetree.txt
	      Debug file giving the complete parse tree of the GDL source file.

       dbg_ruleprec.txt
	      Debug file that lists the rules in precedence order (order in which they will be tested) for each pass.

       $_temp.gdl
	      Debug file containing the output of gdlpp

Author
       Martin Hosken <mhosken@users.sourceforge.net>

							   $Date: 2012-05-29 11:36:50 $ 					     grcompiler(1)
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