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Full Discussion: sed parser behaving strange on replacing multiple words in multiple files
Top Forums Shell Programming and Scripting sed parser behaving strange on replacing multiple words in multiple files Post 303008983 by sammy777888 on Friday 8th of December 2017 04:43:52 AM
Old 12-08-2017
sed parser behaving strange on replacing multiple words in multiple files
I have 4000 files like

Code:
$cat clus_grp_seq10_g.phy 

 18 1002
anig_OJJ65951_1     ATGGTTTCGCAGCGTGATAGAGAATTGTTTAGGGATGATATTCGCTCGCGAGGAACGAAGCTCAATGCTGCCGAGCGCGAGAGTCTGCTAAGGCCATATCTGCCAGATCCGTCTGACCTTCCACGCAGGCCACTTCAGCGGCGCAAGAAGGTTCCTCG
aver_OOF92921_1     ATGGTTTCGCAACGAGAT---------AGAGAATTGAATATCACGGCTTCCTCAGGGGTCTCTGGCATTATGCTGGTGCTCAGATGAGGTTTGGC
anid_EAW13573_1     ATGGTCTCACAGCGTGACAGAGAGTTGGCTGTTGAATACCAGGGCTATCTCAGGGGTTTGTGGCATTACGCTGGGGCCCAGATGCGATTTGGC
azon_EAW20028_1     ATGGCCCTAGCACGTGATAGAGAATTACTGAGGGACACTATTCGCACCCAAGGGACCGCACTTACTGCTGCCGATCGCGAAAATATCCTGAAGCCATATCTGCCGGATCCATCAGAACTTGCACGTCGGCCACTACAGCGACAGAAGAAAGC
awen_EED46037_1     ATGGTATCACAACGGGATAGAGTGGTGTGTCTGCC------------------------------------------------CTCTACAGGTCA------AAACAGTGCGAAATA---------AA
acar_EAL84889_1     ATGGCCCT
akaw_EAWE3573_1     ---------ATGGTCTCAC---------AGCGTGACAGAGAGT---------TGGCTGTTGAATACCAGGGCTATCTCAGGGGTTTGTGGCATTACGC

I want to replace 7 patterns (aver, anid, anig, acar, azon, awen, akaw) in all the files. The resulting file should be like (No change in file name)


Code:
$cat clus_grp_seq10_g.phy 

 18 1002
anig     ATGGTTTCGCAGCGTGATAGAGAATTGTTTAGGGATGATATTCGCTCGCGAGGAACGAAGCTCAATGCTGCCGAGCGCGAGAGTCTGCTAAGGCCATATCTGCCAGATCCGTCTGACCTTCCACGCAGGCCACTTCAGCGGCGCAAGAAGGTTCCTCG
aver     ATGGTTTCGCAACGAGAT---------AGAGAATTGAATATCACGGCTTCCTCAGGGGTCTCTGGCATTATGCTGGTGCTCAGATGAGGTTTGGC
anid     ATGGTCTCACAGCGTGACAGAGAGTTGGCTGTTGAATACCAGGGCTATCTCAGGGGTTTGTGGCATTACGCTGGGGCCCAGATGCGATTTGGC
azon     ATGGCCCTAGCACGTGATAGAGAATTACTGAGGGACACTATTCGCACCCAAGGGACCGCACTTACTGCTGCCGATCGCGAAAATATCCTGAAGCCATATCTGCCGGATCCATCAGAACTTGCACGTCGGCCACTACAGCGACAGAAGAAAGC
awen     ATGGTATCACAACGGGATAGAGTGGTGTGTCTGCC------------------------------------------------CTCTACAGGTCA------AAACAGTGCGAAATA---------AA
acar     ATGGCCCT
akaw     ---------ATGGTCTCAC---------AGCGTGACAGAGAGT---------TGGCTGTTGAATACCAGGGCTATCTCAGGGGTTTGTGGCATTACGC

I wrote a bash script for this
Code:
#!/bin/bash
j=1
for ((i=0;i<=4000;i++));
do
echo "$j"

sed -e s/'aver_[^ ]*'/aver/g clus_grp_seq"$j"_g.phy | sed -e s/'anid_[^ ]*'/anid/g | sed -e s/'anig_[^ ]*'/anig/g | sed -e s/'acar_[^ ]*'/acar/g | sed -e s/'azon_[^ ]*'/azon/g | sed -e s/'awen_[^ ]*'/awen/g | sed -e s/'akaw_[^ ]*'/akaw/g -> clus_grp_seq"$j"_g.phy
wait
let j++
done

but the parser is making several files completely blank. In the folder some files like clus_grp_seq2000_g.phy does not exists, in such case blank file like clus_grp_seq2000_g.phy is OK. But in cases even the file exists in the folder like clus_grp_seq10_g.phy as shown above the parser is making blank files.
Please let me know the problem or suggest an alternative solution.
 

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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)
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