Programming :: Compare Two Files Using Perl Or Shell Scripting?
Mar 8, 2010
I want to compare the following two tab-delimited .txt files (both were subsets of the original files) by comparing Columns 3 and 4 simultaneously. It is easy to compare C3 because both C3s are just numbers. But how to compare C4s?Basically, in File1, "G,G" = G in File2, "C,C" = C in File2, "A,A" = A in File2, "T,T"= T in File2.In File2, A/T in Column4 just equals "A,T" or "T,A" in Column4 of File1. C/T in Column4 just equals "C,T" or "T,C" in Column4 of File1, and etc.
File1:
C1C2 C3C4
ih509rs12345467244750"G,G"
ih499rs6049687244911"C,C"
ih508- 7244977"A,A"
[code]....
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Jul 29, 2010
what command is to be used to call strings from other files to the script and then comparing strings from two different files in the script to check if strings are matched then return the result to another script.
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Oct 27, 2009
I want to compare two files in perl, I have two files file1.txt & file2.txt. if column1 on file2.txt match column1 on file1.txt then I want my result on file3.txt (column1 column2 file1.txt + column1 column2 column3 file2.txt). this problem was solved with "awk" but I want to do in perl.
file1.txt
---------
column1 column2
------- -------
linux-2049 1
linux-2817 1
[code]....
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Nov 19, 2008
I have this program:
#! /usr/bin/perl
use DBI ;
use strict ;
[code]....
and I get this error simply running the program from the command line: DBD::mysql::st execute failed: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '' at line 1 at ./submit.cgi line 24.
is this the right syntax to use, both, for this line:
my (@param) = $cgi->param("firstname","lastname","type") ;
as well as this one:
$sth=$dbh->prepare ("SELECT firstname,lastname,type FROM dts WHERE firstname LIKE $param[0] AND lastname LIKE $param[1] and type LIKE $param[2]" );
or should there be quotes around the $param[0] or something? (also is it $param[0] or $param(0)?)
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Jun 5, 2011
I am trying to create a shell script similar to ls, but which only lists directories. I have the first half working (no argument version), but trying to make it accept an argument, I am failing. My logic is sound I think, but I'm missing something on the syntax.
Code:
if [ $# -eq 0 ] ; then
d=`pwd`
for i in * ; do
if test -d $d/$i ; then
echo "$i:"
code....
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Apr 1, 2010
pretty simple. how would you background a process from a script and get its process id at the same time?
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Oct 13, 2010
I'm writing a Perl script to find an old key in a file and replace it with a new codefirst the program should find the old key in the input file. here is the way I used in my script. but it doesn't work.May you please let me know what is wrong and how I can correct it?the key is stored in the file in the following format:
PHP Code:
Key=("1234567" , someOtherVrable)
I want 1234567
[code]...
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Nov 16, 2009
I have some data ( seperated by semicolon ) with close to 240 rows in a text file temp1. temp2.txt stores 204 rows of data ( seperated by semicolon ). I want to : Sort the data in both files by field1.i.e first data field in every row. compare the data in both files and print out the rows that are not equal in seperate files. I was trying to do this with excel using vlookup, without a great deal of success. hence, i'm exploring the shell script option.
Code:
temp1.txt
1000xyz400100xyzA00680xyz0;19722.83;19565.7;157.13;11;2.74;11.00
1000xyz400100xyzA00682xyz0;7210.68;4111.53;3099.15;216.95;1.21;216.94
1000xyz430200xyzA00651xyz0;146.70;0.00;0.00;0.00;0.00;0.00
[code]....
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Oct 25, 2010
I am trying to read the fields of a file and manipulate them, record by record. Lets say using awk :
awk -F":" `{print $1 $2 $3 $4 $5}' TrackMsgFile.0806`
This prints my fields on screen.But I dont want to print these fields while reading the records instead store them in some variable and manipulate them as per my logic. Does "awk" or some other shell command provides something for this ?
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Jun 19, 2009
I made a little rsync script for log transfer.
Code:
SERVERS=(SERVER1 SERVER2 SERVER3)
SERVER1_SERV=(web ftp mail)
SERVER2_SERV=(web transcoding)
SERVER3_SERV=(web ftp mail)
for SERVER in ${SERVERS[@]}
do
echo "Starting tranfer for server $SERVER"
for SERVICE in ${$SERVER_$SERVICE[@]}
do
something_to_be_done
fi
done
But when I run it I get ${$SERVER_$SERVICE[@]}: bad substitution
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Sep 5, 2010
How do I create a user account in a shell script? I know this may sound n00bish to you, but I know it's more than just mkdir-ing the home directory and subdirectories.
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Dec 2, 2010
I need to part a string into separate integers ....like "0x0-0xffffffff,0x20000" into 3 integers 0x0 and 0xfffffff and 0x20000.... i can't use any other high-level languages ..
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Mar 15, 2011
I got two cgi shell scripting files. Is it possible when i am in file 1, to call a function from file 2?
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Feb 3, 2010
How do i make my strings case-insensitive while comparing them with an if statement?
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Mar 11, 2011
I have a QNX machine with a slinger webserver running on it. With a cgi script i'm trying to do the QNX cksum call and compare it's output value with a fixed output. When i execute the script at the command line it works perfect, but when execute this script by by the webserver in my browser it doesn't work. Here's my code:
#!/bin/sh
FILE="/home/checkfile"
ORIGCHECK="1712885500"
[code].....
Could it be possible that i'm not allowed to do the cksum call in combination with the slinger webserver?
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Jul 3, 2011
so I wrote a simple script to scrape whatsmyip.org for my public IP address and then email it to me if it has changed. I set this up as a cron job ever 30mins.the problem is, it works for about 18 hours and then will have an issue where it says "line 33: [: too many arguments" Which line 33 happens to be my if statement. Now like I said it works fine for about 18 hours, i run the script with 2>&1 to a .out file so i can see what its doing...this is the output of the .out file, the "xxx" does actually show the ip.."PHP Code:
xxx.xxx.xxx.xxx
already in file
xxx.xxx.xxx.xxx
[code]....
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Sep 21, 2010
I am running an application called QuantiSNP [URL]. The binary file is "quantisnp2", called upon in the "run_quantisnp2.sh" supplied by the authors. I am only able to run the application for single file processing (e.g. 1 input file for 1 sample; I can't run the batch file processing because I don't have the necessary BeadStudio report files, which has different formatting for the input files).
The difficulty is that I have 300 samples (300 unique sample IDs) and 3 input files for each sample for a total of 900 runs of this application. I am wondering how would I be able to automate this process as a shell script instead of basically manually changing the sample ID and respective input files every time a run completes? I bolded the single file processing shell script command line options below that need to be changed for each sample/input single file processing run. The command line option "--sampleid" is for the name given to the processed output files corresponding to the sample of interest and there are 3 input files for each sample.
/home2/jason/QuantiSNP/quantisnp/linux64/run_quantisnp2.sh /home2/jason/QuantiSNP/MCR/v79/ --config /home2/jason/QuantiSNP/quantisnp/config/params.dat --levels /home2/jason/QuantiSNP/quantisnp/config/levels-affy.dat --outdir /home2/jason/QuantiSNP/quantisnp_out/ --sampleid sample1 --gender female --input-files /home2/jason/files/sample1_input.txt
Note that each sample has 3 input files, for a total of 3 runs of "quantisnp2" for each sample. e.g.
SAMPLEID INFILE
sample1 /home2/jason/files/sample1_input.txt
sample1 /home2/jason/files/sample1_input2.txt
sample1 /home2/jason/files/sample1_input3.txt
[code]....
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Apr 5, 2011
I am trying to modify a script for research purposes and am having difficulty here as I have little prior experience with C-shell scripting.
The script looks as follows (it includes tcl commands like runFEP that you can ignore)
#!/bin/bash
for ((old=1, new=2; old<=4; old++,new++))
a1=${old}%50
a2=${new}%50
do
cat > input${new}.conf <<EOF
${a1}
code....
My question: I keep getting a syntax error when defining my two variables a1 and a2. I essentially need these variables to be
a1 = value of variable old divided by 50
a2 = value of variable new divided by 50
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Jun 24, 2011
I'm writing a script and I have doubts on how to assign values to an already established variable. The value for the vatriable would be coming from a file with three columns. I'm using the awk command for this. Am I doing it correctly? which of the following two ways is the better one or if both are wrong which one should I use?
#!/bin/nsh
inputfile=$1
rolename=$2
[code]....
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Nov 6, 2010
The two shell scripts (t1prog and t2prog) are given below they are working fine. The input for the first program is 't1.det' and for second program is 't1.rnaml'. These two input files are in 'dir1' folder. I am executing the shell like 'sh t1prog > t1out' and 'sh t2prog > t2out' from this directory only. Then I am executing a java program 'java RNA'; for this, t1out and t2out are input files used in the program and I am getting the final output on screen.
The input files 't1.det' and 't1.rnaml' are in different folders with same name and with different values. Each folder specifies one gene sequence input files.
In mfold directory there are 5 directors and each directory contains these input files as shown below
cd mfold
dir1 dir2 dir3 dir4 dir5
cd dir1
t1.det t1.rnaml
[Code].....
for inputs in different directories and executing these and redirecting the final ouput after executing 'java RNA' statement to a file is needed.
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Mar 21, 2011
Examples:
Code:
$ ./test.sh -a -c 2
operator is -gt
remcount is
^ value missing!
Code:
$ ./test.sh -b -c 2
operator is -lt
remcount is
^ value missing!
Yet when "-c" is the first argument, its value is present:
Code:
$ ./test.sh -c 2 -b
operator is -lt
remcount is 2
What could I do to ensure the value of "-c" is picked up regardless of the argument order?
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Sep 6, 2010
I have two files, uploads.txt and downloads.txt. I would like to combine the columns of these files based on the ip address. How can I best do this?
Uploads.txt Code: 192.168.0.147 1565369
192.168.0.13 1664855
192.168.0.6 1332868 Downloads.txt Code: 192.168.0.147 9838820
[code]...
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Jul 22, 2011
I have written the following script in my linux server to add users for LDAP database.But i can't able to run this.
The script is as following
#!/bin/bash
echo "Mention the username which you want to convert LDIF format"
read username
if ["$username" -e "/ldiffile/passwd"]; then
echo "Username already exists"
else
cat /etc/passwd | grep -i "$username" >> /ldiffile/passwd
fi
The output which i got :
. ldapadd.sh
Mention the username which you want to convert LDIF format
yal2361
-bash: [yal2361: command not found
please let me know where need to change and what
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Nov 8, 2010
I want to find maximum length file in a given directory. It should search recursivley. I want this to be done using ls and simple looping constructs.
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Jul 16, 2011
Dear expertsI have files like
ABD : 5869 events, relative ratio : 1.173800E-01 , sum of ratios : 1.173800E-01
VBD : 12147 events, relative ratio : 2.429400E-01 , sum of ratios : 3.603200E-01
SDF : 17000 events, relative ratio : 3.400000E-01 , sum of ratios : 7.003200E-01
[code]....
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Mar 28, 2011
I have two files with user DN's that exported from two different LDAP directories. I wanted to write a script that reads(checks) users (cn=user1) in file Ack to see if users(cn=user1) exists in file B and give me nice output with what users are missing in file B.I have around 30k users in file A with following format..Quote:
cn=user1,ou=some,o=org
cn=user2,ou=some,o=org
cn=user3,ou=some,o=org
[code]...
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Sep 4, 2010
i used ldap for authentication.now i have a perl script that users use it for login(contact.pl),then this script calls a shell script(ip.sh) for create iptables chain.
when i call that into contact.pl ,it just prints: usr/sbin/iptables but ip chains didn't change.what is problem? whenever run ip.sh in bash it works correctly
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Nov 5, 2010
I would like to compare two md5sum outputs to see if the files match. in my script I have
Code:
ORG_FILE="/path/to/org/file.zip"
NEW_FILE="path/to/new/file.zip"
MD5_ORIG=$(md5sum -b "$ORG_FILE")
[code]....
How do I get just the MD5 hash and not the */.... stuff so I can compare them. i tried Code: JUST_HASH=${$MD5_ORIG:0:32} but All I get is
dir_mon_notify.sh: line 79: ${$MD5_ORIG:0:32}: bad substitution
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Oct 4, 2010
I need to create a script that will compare the differences between two folders and then to copy only the updated and new files only to another directory. I know I need to use rsync here, I can write scripts so really it not how to create a script it is how do I accomplish the transfer of only new or changes files between two folders to a new file. Do I need to link these two folders first and then use the "--compare-dest" switch.
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Nov 29, 2010
when I execute the command from the shell command line - it works and no error code.if I do the exact same command from a perl file - it fails with code 32512.the file is created from the same perl script that runs the command that fails. file permission is 0664.
Code:
#! /usr/local/pkg/perl-5.8.8/bin/perl
print "Content-type: text/html
[code]...
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