01-03-2011
sed command to remove characters help!
I am trying to analyse a large file of sequencing data, example of first 10 lines below,
@HWUSI-EAS656_0044_FC:7:1:2447:1039#GCAATT/1
GNCTATGGCTTGCCGGGCTCAGGGAAGACAATCATAGCCATGAAAATCATGGAAAAGATCAGAAAAACATTTCAA
+HWUSI-EAS656_0044_FC:7:1:2447:1039#GCAATT/1
VBVZVSVZZ[aaW^^aaZ\WdacdaWXYK\SEFZFLTMHSZ^]^YYFHRSacWWcBBBBBBBBBBBBBBBBBBBB
@HWUSI-EAS656_0044_FC:7:1:2632:1042#ATAGTA/1
TNGTACATCTAAAAGCTCTAGAAAAAAAGGAAGCAAATTCACCCAAGAGGAGTAGATGGCAGGAAATAATCAAAC
+HWUSI-EAS656_0044_FC:7:1:2632:1042#ATAGTA/1
NBVWP]Y_]`dbacfggggegegggg``ecaacffcfffcdffff^ffccdfacf^^cac\dadaffcccff\da
@HWUSI-EAS656_0044_FC:7:1:2977:1039#ACCACT/1
ANGTAGCCATCTTTTTACTTTTTAATATGTGGCAGGATATCATTAAGTTGCCTGGGCTAAGGGCTGAGAGGATGA
In order to run the data through the barcoding file I need to remove the letters between characters including # until the /1
I have tried using
sed 's/#*\/1$/\/1/g' <./s_7_sequence.txt >./s_7.txt
to save the data as a new file called s_7.txt without the #***** but whenever I run this it runs but the new file looks exactly the same as the old. I have tried running sed to remove anything to check I'm not being completely useless and have had success with
sed 's/#G//g' <input >output
and this works fine but
obviously only removes the # and the first letter from the lines with #G.
I would appreciate any help at all to correct my sed command, I have now tried as many variations as I can understand but am a complete newby at this.
Thanks
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LEARN ABOUT DEBIAN
shtool-subst
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)