Help with Script Post: 302333914

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Top Forums Shell Programming and Scripting Help with Script Post 302333914 by zajtat on Tuesday 14th of July 2009 10:48:04 AM

07-14-2009

Registered User

Sorry, I will post one of my non-working scripts!
I do apologize!

---------- Post updated at 09:46 AM ---------- Previous update was at 08:59 AM ----------

Oh, I need to rephrase a bit the task:
the are several original files named Pattern1_right_sorted, Pattern2_right_sorted etc and I also need a filed saying the number of the pattern, so the new file should look like this:
number of the pattern (e.g.1) rs1 newFiled g
number of the pattern (e.g. 2) rs2 newField r etc

Here's my non-working script:

Code:

for i in `ls *_right_sorted | cut "_" -f1`;
do
a = wc  -l ${i}_right_sorted;
seq a > ${i}.sequence;
awk `$1 == "rs" {print $8} ${i}_right_sorted > ${i}_field8;
echo `${i} | cut -d "pattern" -f2`> ${i}.number;
join ${i}.number ${i}.sequence ${i}_field8;  
done

Unfortunatelly, this one doesn't work and doesn't add afield of rs1 rs2 etc

Sorry I'm not able to write a better script...

---------- Post updated at 09:48 AM ---------- Previous update was at 09:46 AM ----------

oh,
the last task should actually be

Code:

join ${i}.number ${i}.sequnce ${i}_field8 >${i}_output

Last edited by vgersh99; 07-14-2009 at 12:41 PM.. Reason: code tags, PLEASE!

zajtat

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comm

COMM(1) 							   User Commands							   COMM(1)

NAME

       comm - compare two sorted files line by line

SYNOPSIS

       comm [OPTION]... FILE1 FILE2

DESCRIPTION

       Compare sorted files FILE1 and FILE2 line by line.

       When FILE1 or FILE2 (not both) is -, read standard input.

       With  no  options,  produce three-column output.  Column one contains lines unique to FILE1, column two contains lines unique to FILE2, and
       column three contains lines common to both files.

       -1     suppress column 1 (lines unique to FILE1)

       -2     suppress column 2 (lines unique to FILE2)

       -3     suppress column 3 (lines that appear in both files)

       --check-order
	      check that the input is correctly sorted, even if all input lines are pairable

       --nocheck-order
	      do not check that the input is correctly sorted

       --output-delimiter=STR
	      separate columns with STR

       --total
	      output a summary

       -z, --zero-terminated
	      line delimiter is NUL, not newline

       --help display this help and exit

       --version
	      output version information and exit

       Note, comparisons honor the rules specified by 'LC_COLLATE'.

EXAMPLES

       comm -12 file1 file2
	      Print only lines present in both file1 and file2.

       comm -3 file1 file2
	      Print lines in file1 not in file2, and vice versa.

AUTHOR

       Written by Richard M. Stallman and David MacKenzie.

REPORTING BUGS

       GNU coreutils online help: <http://www.gnu.org/software/coreutils/>
       Report comm translation bugs to <http://translationproject.org/team/>

COPYRIGHT

       Copyright (C) 2017 Free Software Foundation, Inc.  License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent permitted by law.

SEE ALSO

       join(1), uniq(1)

       Full documentation at: <http://www.gnu.org/software/coreutils/comm>
       or available locally via: info '(coreutils) comm invocation'

GNU coreutils 8.28						   January 2018 							   COMM(1)