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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 SUNOS

gst-launch-ext

gst-launch-ext-0.8(1)						   User Commands					     gst-launch-ext-0.8(1)

NAME

       gst-launch-ext-0.8, gst-launch-ext - run a predefined GStreamer pipeline

SYNOPSIS

       gst-launch-ext-0.8 filename [filename...] [gst-std-options]

       gst-launch-ext filename [filename...] [gst-std-options]

DESCRIPTION

       gst-launch-ext-0.8  runs  a  basic predefined GStreamer pipeline, and prints the name of the pipeline. gst-launch-ext-0.8 is only used as a
       quick test to ensure that codecs and GStreamer work properly. gst-launch-ext-0.8 does not handle more advanced features	such  as  synchro-
       nization.

OPTIONS

       The following options are supported by gst-launch-ext-0.8 and gst-launch-ext:

       gst-std-options		       Standard  options  available  for  use  with  most GStreamer applications.  See gst-std-options(5) for more
				       information.

       The following options are supported by gst-launch-ext only:

       --gst-list-mm   List found major/minor versions. This option displays the versions that are available.

       --gst-mm=string Force major/minor version. This option enables you to specify a specific version to run, if you do  not	want  to  run  the
		       default version.

       --print	       Print wrapped command line. This option displays the command that will be run, and then runs the command.

OPERANDS

       The following operands are supported:

       filename        The name of the GStreamer pipeline to run.

EXTENDED DESCRIPTION

       gst-launch-ext-0.8  can	be  configured by creating a .gst file in your home directory. This PERL-style configuration file can override the
       default values for audio and video output sinks.

       The following example .gst file implements the same defaults as those hard-coded in the script:

       AUDIOSINK = osssink
       VIDEOSINK = ffmpegcolorspace ! xvimagesink

       You can change osssink to esdsink, alsasink, or sunaudiosink, and you can change xvimagesink to ximagesink, aasink,  or	sdlvideosink.  You
       must have the appropriate plugin installed on the system to use the specified output sink. Other GStreamer plug-ins can also be used.

EXAMPLES

       Example 1: Launching a GStreamer Pipeline

       example% gst-launch-ext-0.8 filename

EXIT STATUS

       The following exit values are returned:

       0	Application exited successfully

       >0	Application exited with failure

FILES

       The following files are used by this application:

       /usr/bin/gst-launch-ext-Executable to run a predefined GStreamer pipeline

ATTRIBUTES

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

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWgnome-media		   |
       +-----------------------------+-----------------------------+
       |Interface stability	     |External			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       Latest version of the GNOME Desktop User Guide for your platform.

       gst-complete(1),  gst-compprep(1),  gst-feedback(1),  gst-inspect(1), gst-launch(1), gst-md5sum(1), gst-register(1), gst-thumbnail(1), gst-
       typefind(1), gst-xmlinspect(1), gst-xmllaunch(1), gstreamer-properties(1), libgstreamer-0.8(3), libgstgetbits(3), gst-std-options(5)

NOTES

       Written by Brian Cameron, Sun Microsystems Inc., 2004.

SunOS 5.10							    14 Oct 2004 					     gst-launch-ext-0.8(1)
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