Login or Register to Ask a Question and Join Our Community

Sponsored Content
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.
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

renaming multiple files while replacing string

hi, i've found a few examples of scripts to do this but for some reason can't get them to work properly. basically i have some dirs with a few hundred files mixed in with a bunch of other files that were made with a typo in part of them. long-file-names-tyo-example.ext want to be able... (2 Replies)
Discussion started by: kevin9
2 Replies

2. Shell Programming and Scripting

Replacing string in multiple files

Hi, I need to replace the string 'abcd' with 'xyz' in a file sample.xml This sample.xml is also present in the subdirectories of the current directory. Eg, If I am in /user/home/ the sample.xml if present in /user/home/ /user/home/folder1/ /user/home/folder2/... (3 Replies)
Discussion started by: arulanandsp
3 Replies

3. Shell Programming and Scripting

Replacing text from multiple files at multiple location

Hi, I have many files scattered in all different folders. I want to replace the text within all the files using a single command ( awk, sed...) Is it possible? example find all the files in which there is text "memory" and replace it with "branded_memories". the files can be at the... (2 Replies)
Discussion started by: rudoraj
2 Replies

4. UNIX for Dummies Questions & Answers

best method of replacing multiple strings in multiple files - sed or awk? most simple preferred :)

Hi guys, say I have a few files in a directory (58 text files or somthing) each one contains mulitple strings that I wish to replace with other strings so in these 58 files I'm looking for say the following strings: JAM (replace with BUTTER) BREAD (replace with CRACKER) SCOOP (replace... (19 Replies)
Discussion started by: rich@ardz
19 Replies

5. Shell Programming and Scripting

Counting occurrences of all words in multiple files

Hey Unix gurus, I would like to count the number occurrences of all the words (regardless of case) across multiple files, preferably outputting them in descending order of occurrence. This is well beyond my paltry shell scripting ability. Researching, I can find many scripts/commands that... (4 Replies)
Discussion started by: twjolson
4 Replies

6. Shell Programming and Scripting

How to count the number of occurrence of words from multiple files?

File 1 aaa bbb ccc File 2 aaa xxx zzz bbb File 3 aaa bbb xxx Output: (4 Replies)
Discussion started by: Misa-Misa
4 Replies

7. Shell Programming and Scripting

USING sed to remove multiple strings/words from a line

Hi I use sed comnand to remove occurance of one workd from a line. However I need to removed occurance of dufferent words in ne line. Original-1 Hi this is the END of my begining Comand sed s/"END"/"start"/g Output-1 Hi this is the start of my beginig But I have more... (9 Replies)
Discussion started by: mnassiri
9 Replies

8. Shell Programming and Scripting

Replacing old TNS entries with New one in multiple files

I have requirement to replace old TNS entries with New one in multiple files. one file may contain more then one occurrence of tns. Example: Below is the one of occurrence in a current file(s). i am interested to replace only red part. <connection-pool name="Google_APP_CP"... (4 Replies)
Discussion started by: KDDubai333
4 Replies

9. Shell Programming and Scripting

Replacing matched patterns in multiple files with awk

Hello all, I have since given up trying to figure this out and used sed instead, but I am trying to understand awk and was wondering how someone might do this in awk. I am trying to match on the first field of a specific file with the first field on multiple files, and append the second field... (2 Replies)
Discussion started by: karlmalowned
2 Replies

10. UNIX for Beginners Questions & Answers

Issue with search and replacing multiple items in multiple files

Im having an issue when trying to replace the first column with a new set of values in multiple files. The results from the following code only replaces the files with the last set of values in val.txt. I want to replace all the files with all the values. for date in {1..31} do for val in... (1 Reply)
Discussion started by: ncwxpanther
1 Replies

LEARN ABOUT DEBIAN

smp_conf_route_info

SMP_CONF_ROUTE_INFO(8)						     SMP_UTILS						    SMP_CONF_ROUTE_INFO(8)

NAME

       smp_conf_route_info - invoke CONFIGURE ROUTE INFORMATION SMP function

SYNOPSIS

       smp_conf_route_info [--disable] [--expected=EX] [--help] [--hex] [--index=IN] [--interface=PARAMS] [--phy=ID] [--raw] [--routed=R_SAS_ADDR]
       [--sa=SAS_ADDR] [--verbose] [--version] SMP_DEVICE[,N]

DESCRIPTION

       Sends a SAS Management Protocol (SMP) CONFIGURE ROUTE INFORMATION function request to a SMP target. The SMP target  is  identified  by  the
       SMP_DEVICE  and	the  --sa=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 CONFIGURE ROUTE INFORMATION function is associated with a phy-based route table. The REPORT ROUTE
       INFORMATION function is provided to report phy-based route table entries.

       Each phy in a SAS expander that has an associated routing attribute of "table" has a router table. The number of rows (or entries) in  each
       router table is given by the "expander route indexes" field in the response of the REPORT GENERAL function.

OPTIONS

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

       -d, --disable
	      set  the	"disable expander route entry" flag in a row of the router table associated with --phy=ID of the given SMP target (e.g. an
	      expander).  Within the router table the row that is disabled is identified by the expander route index given by --index=IN.

       -E, --expected=EX
	      set the 'expected expander change count' field in the SMP request.  The value EX is from 0 to  65535  inclusive  with  0	being  the
	      default  value.  When  EX is greater than zero then if the value doesn't match the expander change count of the SMP target (i.e. the
	      expander) when the request arrives then the target ignores the request and sets a function result of "invalid expander change count"
	      in the response.

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

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

       -i, --index=IN
	      expander	route  index.  IN  is  a  value  between  0  and  65535.  Default  is  0.   More  precisely  the  maximum  index  value is
	      (expander_route_indexes - 1).

       -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.

       -p, --phy=ID
	      phy identifier. ID is a value between 0 and 254. Default is 0.

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

       -R, --routed=R_SAS_ADDR
	      specifies the SAS address to be placed in a row (given by --index=IN) of the router table associated with --phy=ID. Default value is
	      0.  The R_SAS_ADDR is in decimal but most SAS addresses are given in hexadecimal. To give a number in hexadecimal either	prefix	it
	      with '0x' or put a trailing 'h' on it.

       -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 CONFIGURE ROUTE INFORMATION function was introduced in SAS-1 .  The "Expander change count" field was added in SAS-2 .

AUTHORS

       Written by Douglas Gilbert.

REPORTING BUGS

       Report bugs to <dgilbert at interlog dot com>.

COPYRIGHT

       Copyright (C) 2006-2011 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_general, smp_rep_route_info(smp_utils)

smp_utils-0.96							     May 2011						    SMP_CONF_ROUTE_INFO(8)
All times are GMT -4. The time now is 10:33 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy