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Full Discussion: Run sed and awk in multiple files in adirectory
Top Forums Programming Run sed and awk in multiple files in adirectory Post 303018397 by Dieunel on Tuesday 5th of June 2018 11:17:11 AM
Old 06-05-2018
Saludos


I edited the script as suggested but I still have empty output, here is the report :
Code:
$ ls -sh
total 317M
148M ERR598955_orfm.fna.1   16M ERR598955_orfm.fna.1.test  149M ERR598955_orfm.fna.2  5.3M ERR598955_orfm.fna.2.test  4.0K sov.sh

Code:
[dderilus@boqueron test]$ cat sov.sh 
#!/bin/bash
fmask="ERR598955_orfm.fna"
for f in $fmask.*
do
  [ -f "$f" ] || continue # ensure this is an existing file
  ext=${f#$fmask} # strip off the leading fmask
  ext=${ext#.} # strip off a leading dot
  pattern=$(awk '{x=$1} END {print x}' "$f") # pattern is the 1st word in the last line
  newfile=first_out.$ext
  sed -n '1,/'"${pattern}"'/d; /^>/,$p' "$f" > "$newfile"
done

Code:
[dderilus@boqueron test]$ /bin/bash -x sov.sh 
+ fmask=ERR598955_orfm.fna
+ for f in '$fmask.*'
+ '[' -f ERR598955_orfm.fna.1 ']'
+ ext=.1
+ ext=1
++ awk '{x=$1} END {print x}' ERR598955_orfm.fna.1
+ pattern=GGSSFMGCPSSVMSPASGYSKPAIILNSVVHPIKDDPPHKRSVNTVFQNYALFPHMTVSQNIG
+ newfile=first_out.1
+ sed -n '1,/GGSSFMGCPSSVMSPASGYSKPAIILNSVVHPIKDDPPHKRSVNTVFQNYALFPHMTVSQNIG/d; /^>/,$p' ERR598955_orfm.fna.1
+ for f in '$fmask.*'
+ '[' -f ERR598955_orfm.fna.1.test ']'
+ ext=.1.test
+ ext=1.test
++ awk '{x=$1} END {print x}' ERR598955_orfm.fna.1.test
+ pattern=ERR598955.61408_2_2_1
+ newfile=first_out.1.test
+ sed -n '1,/ERR598955.61408_2_2_1/d; /^>/,$p' ERR598955_orfm.fna.1.test
+ for f in '$fmask.*'
+ '[' -f ERR598955_orfm.fna.2 ']'
+ ext=.2
+ ext=2
++ awk '{x=$1} END {print x}' ERR598955_orfm.fna.2
+ pattern=LSEKKSSQNPLLFSICLIFFWTTFLILPEKAFWRV
+ newfile=first_out.2
+ sed -n '1,/LSEKKSSQNPLLFSICLIFFWTTFLILPEKAFWRV/d; /^>/,$p' ERR598955_orfm.fna.2
+ for f in '$fmask.*'
+ '[' -f ERR598955_orfm.fna.2.test ']'
+ ext=.2.test
+ ext=2.test
++ awk '{x=$1} END {print x}' ERR598955_orfm.fna.2.test
+ pattern=ERR598955.712540_97_1_3
+ newfile=first_out.2.test
+ sed -n '1,/ERR598955.712540_97_1_3/d; /^>/,$p' ERR598955_orfm.fna.2.test
[dderilus@boqueron test]$ ls -sh
total 317M
148M ERR598955_orfm.fna.1   16M ERR598955_orfm.fna.1.test  149M ERR598955_orfm.fna.2  5.3M ERR598955_orfm.fna.2.test     0 first_out.1     0 first_out.1.test     0 first_out.2     0 first_out.2.test  4.0K sov.sh


Regards
Last edited by rbatte1; 06-05-2018 at 12:25 PM.. Reason: Added CODE tags
 

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LEARN ABOUT OPENSOLARIS

lptest

lptest(1B)					     SunOS/BSD Compatibility Package Commands						lptest(1B)

NAME

       lptest - generate line printer ripple pattern

SYNOPSIS

       /usr/ucb/lptest [length [count]]

DESCRIPTION

       The  lptest  utility  writes the traditional ripple test pattern to the standard output. In 96 lines, the ripple test pattern prints all 96
       printable ASCII characters in each position. The ripple test pattern was originally created to test printers.  It is also useful for  test-
       ing terminals, driving terminal ports, debugging, and performing tasks that require a quick supply of random data.

       This command is obsolete.

OPTIONS

       length	 Specifies the length of the output line in characters. 79 characters is the default.

       count	 Specifies the number of output lines. 200 lines is the default. If  count is specified, length must also be specified.

EXIT STATUS

       The following exit values are returned:

       0	   Successful completion.

       non-zero    An error occurred.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWscplp 		   |
       +-----------------------------+-----------------------------+

SEE ALSO

       attributes(5)

SunOS 5.11							    9 Sep 1996								lptest(1B)
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