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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

smp_rep_exp_route_tbl

SMP_REP_EXP_ROUTE_TBL(8)					     SMP_UTILS						  SMP_REP_EXP_ROUTE_TBL(8)

NAME

       smp_rep_exp_route_tbl - invoke REPORT EXPANDER ROUTE TABLE LIST SMP function

SYNOPSIS

       smp_rep_exp_route_tbl  [--brief]  [--help] [--hex] [--index=IN] [--interface=PARAMS] [--num=NUM] [--phy=ID] [--raw] [--sa=SAS_ADDR] [--ver-
       bose] [--version] SMP_DEVICE[,N]

DESCRIPTION

       Sends a SAS Management Protocol (SMP) REPORT EXPANDER ROUTE TABLE LIST function request	to  a  SMP  target  and  decodes  or  outputs  the
       response.  The  SMP  target is identified by the SMP_DEVICE and the SAS_ADDR.  Depending on the interface, the SAS_ADDR may be deduced from
       the SMP_DEVICE. The mpt interface uses SMP_DEVICE to identify a HBA (an SMP initiator) and needs the additional ,N to differentiate between
       HBAs if there are multiple present.

       There  are two expander route table types: phy-based and expander-based.  The expander-based route table was introduced in SAS-2 and super-
       sedes the phy-based route tables. The REPORT EXPANDER ROUTE TABLE LIST function is associated with an expander-based route table. There	is
       no corresponding CONFIGURE function because a expander-based route table is self-configured.

OPTIONS

       Mandatory arguments to long options are mandatory for short options as well.

       -b, --brief
	      reduce the decoded response output.

       -h, --help
	      output the usage message then exit.

       -H, --hex
	      output the response (less the CRC field) in hexadecimal.

       -i, --index=IN
	      IN is the starting routed SAS address index. The default value is 0.

       -I, --interface=PARAMS
	      interface  specific  parameters.	In this case "interface" refers to the path through the operating system to the SMP initiator. See
	      the smp_utils man page for more information.

       -n, --num=NUM
	      maximum number of descriptors to fetch (default is 62). Note that maximum SMP frame size is 1028 bytes (including a trailing 4  byte
	      CRC) so 62 descriptors is the maximum number that can fit in one response.

       -p, --phy=ID
	      starting	phy  identifier  within  bitmap.  ID should be one of 0 (the default), or a multiple of 48. Note there is only one expnder
	      route table per expander, not one per phy.

       -r, --raw
	      send the response (less the CRC field) to stdout in binary. All error messages are sent to stderr.

       -s, --sa=SAS_ADDR
	      specifies the SAS address of the SMP target device. Typically this is an expander. This option may not be needed if  the	SMP_DEVICE
	      has the target's SAS address within it. The SAS_ADDR is in decimal but most SAS addresses are shown in hexadecimal. To give a number
	      in hexadecimal either prefix it with '0x' or put a trailing 'h' on it.

       -v, --verbose
	      increase the verbosity of the output. Can be used multiple times

       -V, --version
	      print the version string and then exit.

CONFORMING TO

       The SMP REPORT EXPANDER ROUTE TABLE LIST function was introduced in SAS-2 .

AUTHORS

       Written by Douglas Gilbert.

REPORTING BUGS

       Report bugs to <dgilbert at interlog dot com>.

COPYRIGHT

       Copyright (C) 2007-2011 Douglas Gilbert
       This software is distributed under a FreeBSD license. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A  PARTICULAR  PUR-
       POSE.

SEE ALSO

       smp_utils, smp_rep_route_info

smp_utils-0.96							     May 2011						  SMP_REP_EXP_ROUTE_TBL(8)
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