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Top Forums Shell Programming and Scripting sed to remove all lines in file that are not .vcf.gz extention Post 302981836 by RudiC on Tuesday 20th of September 2016 10:48:38 AM
Old 09-20-2016
Code:
sed  '/.vcf.gz$/!d' file
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.genome.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.genome.vcf.gz

Again your spec is incorrect, here in the desired output derived from your input.
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SHTOOL-SUBST.TMP(1)					      GNU Portable Shell Tool					       SHTOOL-SUBST.TMP(1)

NAME
shtool-subst - GNU shtool sed(1) substitution operations SYNOPSIS
shtool subst [-v|--verbose] [-t|--trace] [-n|--nop] [-w|--warning] [-q|--quiet] [-s|--stealth] [-i|--interactive] [-b|--backup ext] [-e|--exec cmd] [-f|--file cmd-file] [file] [file ...] DESCRIPTION
This command applies one or more sed(1) substitution operations to stdin or any number of files. OPTIONS
The following command line options are available. -v, --verbose Display some processing information. -t, --trace Enable the output of the essential shell commands which are executed. -n, --nop No operation mode. Actual execution of the essential shell commands which would be executed is suppressed. -w, --warning Show warning on substitution operation resulting in no content change on every file. The default is to show a warning on substitution operations resulted in no content change on all files. -q, --quiet Suppress warning on substitution operation resulting in no content change. -s, --stealth Stealth operation. Preserve timestamp on file. -i, --interactive Enter interactive mode where the user has to approve each operation. -b, --backup ext Preserve backup of original file using file name extension ext. Default is to overwrite the original file. -e, --exec cmd Specify sed(1) command directly. -f, --file cmd-file Read sed(1) command from file. EXAMPLE
# shell script shtool subst -i -e 's;(c) ([0-9]*)-2000;(c) 1-2001;' *.[ch] # RPM spec-file %install shtool subst -v -n -e 's;^(prefix=).*;1 $RPM_BUILD_ROOT%{_prefix};g' -e 's;^(sysconfdir=).*;1 $RPM_BUILD_ROOT%{_prefix}/etc;g' `find . -name Makefile -print` make install HISTORY
The GNU shtool subst command was originally written by Ralf S. Engelschall <rse@engelschall.com> in 2001 for GNU shtool. It was prompted by the need to have a uniform and convenient patching frontend to sed(1) operations in the OpenPKG package specifications. SEE ALSO
shtool(1), sed(1). 18-Jul-2008 shtool 2.0.8 SHTOOL-SUBST.TMP(1)
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