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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 REDHAT

dos2unix

dos2unix(1)						      General Commands Manual						       dos2unix(1)

NAME

       dos2unix - DOS/MAC to UNIX text file format converter

SYNOPSYS

       dos2unix [options] [-c convmode] [-o file ...] [-n infile outfile ...]

       Options:

       [-hkqV] [--help] [--keepdate] [--quiet] [--version]

DESCRIPTION

       This manual page documents dos2unix, the program that converts plain text files in DOS/MAC format to UNIX format.

OPTIONS

       The following options are available:

       -h --help
	      Print online help.

       -k --keepdate
	      Keep the date stamp of output file same as input file.

       -q --quiet
	      Quiet mode. Suppress all warning and messages.

       -V --version
	      Prints version information.

       -c --convmode convmode
	      Sets conversion mode. Simulates dos2unix under SunOS.

       -o --oldfile file ...
	      Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used.

       -n --newfile infile outfile ...
	      New  file  mode.	Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be
	      used or you WILL lost your files.

EXAMPLES

       Get input from stdin and write output to stdout.

	      dos2unix

       Convert and replace a.txt. Convert and replace b.txt.

	      dos2unix a.txt b.txt

	      dos2unix -o a.txt b.txt

       Convert and replace a.txt in ASCII conversion mode.  Convert and replace b.txt in ISO conversion mode.  Convert	c.txt  from  Mac  to  Unix
       ascii format.

	      dos2unix a.txt -c iso b.txt

	      dos2unix -c ascii a.txt -c iso b.txt

	      dos2unix -c mac a.txt b.txt

       Convert and replace a.txt while keeping original date stamp.

	      dos2unix -k a.txt

	      dos2unix -k -o a.txt

       Convert a.txt and write to e.txt.

	      dos2unix -n a.txt e.txt

       Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt.

	      dos2unix -k -n a.txt e.txt

       Convert and replace a.txt. Convert b.txt and write to e.txt.

	      dos2unix a.txt -n b.txt e.txt

	      dos2unix -o a.txt -n b.txt e.txt

       Convert c.txt and write to e.txt. Convert and replace a.txt.  Convert and replace b.txt. Convert d.txt and write to f.txt.

	      dos2unix -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt

DIAGNOSTICS

BUGS

       The program does not work properly under MSDOS in stdio processing mode.  If you know why is that so, please tell me.

AUTHORS

       Benjamin Lin - <blin@socs.uts.edu.au>

       Bernd Johannes Wuebben (mac2unix mode) <wuebben@kde.org>

MISCELLANY

       Tested environment:

	      Linux 1.2.0 with GNU C 2.5.8

	      SunOS 4.1.3 with GNU C 2.6.3

	      MS-DOS 6.20 with Borland C++ 4.02

       Suggestions and bug reports are welcome.

SEE ALSO

       unix2dos(1) mac2unix(1)

1995.03.31							   dos2unix v3.0						       dos2unix(1)
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