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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 REDHAT

pbmpage

pbmpage(1)						      General Commands Manual							pbmpage(1)

NAME

       pbmpage - create a one page test pattern for printing

SYNOPSIS

       pbmpage [-a4] test_pattern

DESCRIPTION

       pbmpage	generates a one page test pattern to print on a sheet of paper, for use in calibrating a printer.  The test pattern in is PBM for-
       mat.

       pbmpage produces an image intended for 600 dots per inch printer resolution.

       If you are printing on an HP PPA printer, you can convert the output of this program to a stream that you can feed to the printer with pbm-
       toppa.

       Bear  in  mind  that  when you print the test pattern, you are testing not only the printer, but any converter or driver software along the
       printing path.  Any one of these components may adjust margins, crop the image, erase edges, and such.

       If, due to addition of margins, the printer refuses to print the image because it is too big, use pnmcut to cut the right and bottom  edges
       off the test pattern until it is small enough to print.

       test_pattern is the number of the test pattern to generate, as follows.	The default is 1.

       1      A grid ruled in numbers of pixels.  The outermost rules are exactly at the edges of the paper.

       2      A vertical line segment, one pixel wide, extending 1/2" up from the exact center of the page.

       3      Two  diagonal line segments, one starting at the upper left corner of the page, the other starting from the lower left corner of the
	      page.  Both extend 1/2" toward the center of the page at 45 degrees.

OPTIONS

       -a4    Generate an image for A4 (European) paper.  Without this option, pbmpage generates an image for US standard paper (8 1/2" wide x 11"
	      high).

SEE ALSO

       pbmtoppa(1), pnmcut(1), pbm(5)

AUTHOR

       Tim Norman.  Copyright (C) 1998.  Licensed under GNU Public License

       Manual page by Bryan Henderson, May 2000.

								    01 May 2000 							pbmpage(1)
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