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Full Discussion: Grepping one file column from another file
Top Forums Shell Programming and Scripting Grepping one file column from another file Post 302881101 by newbie83 on Thursday 26th of December 2013 03:05:19 PM
Old 12-26-2013
Thanks, but it is not producing any output, what am I doing wrong? I changed $4 to $5, added a new field to dataset

Code:
# cat > inp2.txt
Q0UR51  Q0UR51_PHANO    5973037 XP_001796160.1  111065707: 169605479            GO:0004190; GO:0006508          UniRef100_Q0UR51        UniRef90_Q0UR51 UniRef50_N4XCZ1 UPI0000DD11E3           321614                  18024570        CH445332     EAT86827.1

# cat > inp1.txt
comp100008_c0_seq1      169605479
comp1001565_c0_seq1     326493850
comp10017_c0_seq1       399172251
comp10020_c0_seq1       322703447
comp100416_c0_seq1      115471291
comp10045_c0_seq1       473789509
comp1007987_c0_seq1     357112415
comp100803_c0_seq1      475610100
comp10090_c0_seq1       322706779
comp1009402_c0_seq1     326510337


# awk -F"\t" '
> NR == FNR {
>         n = split($5, f, /:/)
>         for(i = 1; i <= n; i++) o[f[i]] = " " $0
>         next
> }
> {       print $0 o[$2]
> }' inp2.txt inp1.txt
comp100008_c0_seq1      169605479
comp1001565_c0_seq1     326493850
comp10017_c0_seq1       399172251
comp10020_c0_seq1       322703447
comp100416_c0_seq1      115471291
comp10045_c0_seq1       473789509
comp1007987_c0_seq1     357112415
comp100803_c0_seq1      475610100
comp10090_c0_seq1       322706779
comp1009402_c0_seq1     326510337

---------- Post updated at 04:05 PM ---------- Previous update was at 04:04 PM ----------

Quote:
Originally Posted by Don Cragun
Your specification said that field5 had subfields separated by a colon; your real data seems to contain subfields you want to match in fields 5 and 6 separated by a colon and a space. None of the code we provided will work if your input data doesn't match the specifications you supplied.
I`m sorry, if that is the problem I didn't realize it earlier. the space is inconsistent and has to be trimmed.
 

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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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