Perl is a high-level, general-purpose, interpreted, dynamic programming language. It was originally developed by Larry Wall as a general-purpose Unix scripting language to make report processing easier, over a period with support from open source community, it has evolved and matured to be used for ...

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3answers
23 views

Concatenate Sequences under a Heading

I have a file like File1. With a heading for example ">Contig1" and I want to concatenate all the sequences under the respective heading. File1: >Contig1 ACCCCATACATCCAAA NNNNNNNNNNCATACA ...
0
votes
2answers
1k views

Failed dependencies trying to install package 'libxml2'

I am trying to install libxml2, but my system complains about dependencies. The dependent packages exist on system. The ultimate goal is to install xml_grep2, I have been trying various methods ...
3
votes
1answer
41 views

Handling dynamically changing column positions and splitting file

I have a unique problem. I have a file with following columns PersonId, AB1, AB2, AB3, DG1_B1,DG1_B2,DG2 1,0,1,0,3,5,7 2,0,3,1,3,7,4 I want to split this and create multiple files based on the ...
-1
votes
0answers
11 views

calling uglifyjs (javascript function) from within a perl script [migrated]

I have a directory full of .js files and I have already written a perl script that displays the source code from all of the .js files in a new file. The source files in the new file are all separated ...
4
votes
5answers
4k views

extract the 4th column from a csv file using unix command

I have a csv file formatted as below. "col1","col2","col3","col4" "1","text1","<p>big html text</p> ","4th column" "2","text2","<p>big2 html2 text2</p> ...
0
votes
1answer
32 views

Kill a Process for a User [closed]

chomp $choice; if ($choice == 5) { print "**********************************\n"; print " Enter the User Name\n"; $user_name = <STDN>; sub kill_processes { $user_name = ...
1
vote
1answer
102 views

“Requires: perl(:MODULE_COMPAT_5.8.8)”

I use CentOS 6.5 for my server with below repository: IUS epel ces-standard-* base/upgrade/extras When I tried to update today (it's been a while I haven't updated this server), I got the ...
2
votes
3answers
29 views

Delete until given character starting from given string

root@server:~/foo$ cat INPUT.txt limit. Current u'^'ZO limit. Current usage'^'FR limit. Current us'^'AS limit. Current usage 95 %.'^'FR limit. Cur'^'AEW root@server:~/foo$ sed ...
0
votes
1answer
26 views

Bandwidth speed test with nginx

I have server with nginx-1.4.1. I want to test bandwidth between my desktop and server. Incoming speed I can test by simple download file with size 10M from server and count time what I need to ...
0
votes
0answers
32 views

Unable to install Crypt::SSLeay perl module on RHEL 5.7 (x86_64)

Here is the scenario, actually my RHEL 5.7 (x64_86) server don't have internet connection. but I want to install Crypt::SSLeay perl module on that server. So I downloaded it from CPAN & then ...
0
votes
0answers
5 views

Group Already Exist [migrated]

#!/usr/bin/perl use strict; use warnings; my $group_name = <STDIN>; my $group_id = <STDIN>; my $choice = <STDIN>; print "* My menu *\n"; print "* *\n"; print "* 1. Create a ...
4
votes
1answer
34 views

grep variable-length optional text

I would like to search for edge-anchored text that has a block of preceding optional text, any amount of which can be included in the match. For instance, supposing I am trying to find ^xyz but would ...
0
votes
3answers
519 views

compare two files based on a column and print it

I have two big files of 400,000 lines. I want to compare the column 1 of the second file with column 1 of first file recursively. If they match I would like to print the whole line. It is a sorted ...
0
votes
2answers
74 views

how to remove all double quotes from csv except specific field

I want to remove all double quotes from my csv but not the fourth field (because the four fields represent PATH of file) Please advice how to implement this by sed or awk or perl one liner , etc ...
5
votes
2answers
275 views

How is the inplace modification of a file being done?

What does the "inplace" modification of a file e.g. via sed -i or perl -i mean? My question is about how this inplace modification is done. Is the file copied the modification is done in the copy and ...
2
votes
2answers
113 views

Format the content of the file using Perl

I am new to Perl programming and I am stuck with this problem for some time. Can you please help me in solving it? I have a file with the following format: >Country1 Aus trali a >Country5 ...
5
votes
1answer
38 views

Count duplicate rows with constraint

I have the following file: A B 1990 A C 2001 A C 2013 A B 2001 B C 2013 A D 2001 A D 2014 I need to count duplicate pairs (in the 1st and 2nd column) and to each such pair assign the lowest value ...
1
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3answers
1k views

Debian Wheezy and perl modules installed into /root not system

I have small problem cause everytime i issue cpan YAML or try to install any perl module it install's it inito /root/perl5 and with this any other user cannot use modules that I've installed as a ...
4
votes
2answers
70 views

Get the maximum sum for a file on 2 keys

I have a file as below. key1 key2 key3 a1 2 l1 a1 2.5 l2 a2 2 l2 a3 2.5 l3 a3 2.1 l4 a3 2.2 l5 I am trying to find the maximum possible sum of key2 that satisfies the ...
0
votes
0answers
48 views

zip command is failing during high memory usage

We have several perl scripts, which generates and emails reports. The script that emails the files expects a .zip extension. The report scripts generates a .txt or .xls file and then runs the ...
1
vote
1answer
402 views

Using EXIFTool to add EXIF data from filenames

There is a set of photos with timestamps in their filenames like these: Photo on 3-09-12 at 9.24 PM #2.jpg Photo on 3-09-12 at 9.24 PM #1.jpg Photo on 3-09-12 at 8.23 PM.jpg etc. ("3-09-12", ...
1
vote
3answers
543 views

compare two columns of different files and print if it matches

I am using solaris 10 and Grep options involving -f doesnt work . I have two pipe separated files: file1: abc|123|BNY|apple| cab|234|cyx|orange| def|kumar|pki|bird| file 2 : abc|123| ...
3
votes
4answers
94 views

How to sort with a delimiter that is several characters long?

INPUT: $ cat a.txt 1FOO2FOO3 4FOO5FOO5 2FOO1FOO9 $ OUTPUT: $ cat a.txt | sort SOMEMAGIC 2FOO1FOO9 1FOO2FOO3 4FOO5FOO5 $ Question: How can I sort, if I have a several character long ...
0
votes
0answers
43 views

Install application on barebone linux board without internet

I'm kind of new to using linux for hardware development. I made a C program which uses ExifTool, and it works fine on the desktop. The ExifTool have to be installed and runs on Perl. I can cross ...
2
votes
1answer
197 views

Convert xml subtitle file to srt format

I have a xml subtitle that looks like this: <?xml version="1.0" encoding="utf-8" ?><transcript> <Item from="1.16" duration="4.68"><![CDATA[(Dong-hyuk is coming to see you now.) ...
1
vote
1answer
44 views

Retrieving fasta sequences using bed file information from locally installed file

I have a .bed file containing around 30000 rows for which I have the sequences retrieved using fetch-sequences module of the rsat tool (http://rsat.ulb.ac.be/rsat/help.fetch-sequences.html#usage). ...
3
votes
3answers
254 views

calculate sum of squares using shell script in perl/awk

I have 2 files as below. file1 0.34 0.27 0.32 file2 0.15 0.21 0.15 Now, I would like to calculate the sum of squares between each column. For example, [(0.34 - 0.15)^2 + (0.27 - 0.21)^2 + ...
3
votes
3answers
101 views

What perl script will scp directory with spaces in name?

I"ve been trying for several hours to figure out how to get perl to scp a directory with a space in the name. I'm currently getting the error scp: ambiguous target Here is the script that is not ...
4
votes
2answers
60 views

Verify line endings from a text created by perl script

I am interested in seeing the contents of a text file in hex mode. I have tried :%!xxd and the problem is that I can not really understand which hex code represents each letter e.g. when you use an ...
4
votes
1answer
103 views

Is building Perl an inside joke or is it supposed to require this many `make` invocations?

So I am building Perl version 5.18.2 from source on an ARMv7 processor right now, a Krait on the Snapdragon S4, and I am not too sure how much support there is for such an architecture. By the way, I ...
1
vote
2answers
69 views

Receiving emails over IMAP and parsing with a script with minimal delay

I have a Perl script that uses NET::IMAPClient and MIME::Parser which simply reads new emails from an IMAP server and saves any attachments to disk. My question is: what is the best way to run this ...
1
vote
0answers
38 views

Some errors have occured when I installed lucene, a perl module!

Some errors have occured when I installed lucene, a perl module: [xlwang@localhost Lucene-0.18]$ make test Running Mkbootstrap for Lucene () chmod 644 Lucene.bs PERL_DL_NONLAZY=1 ...
1
vote
4answers
4k views

sed/awk/perl - delete spaces between two strings/words + solaris 10

please advice how to delete the spaces between "=" to the value/string ( after the "=" character) , should be implemented by awk or sed or perl command and command must to fit for solaris OS , ( ...
10
votes
6answers
355 views

Using Perl to count the number of scientific numbers in a file

How I can count the number of scientific numbers in a file? The file also has a few lines of header which needs to be skipped. A portion of the file's content is in below. FileHeaderLine1 ...
1
vote
1answer
50 views

Extract time stamps and find the difference

I have a large set of logs as shown below: June 5 15:51:56.606 [3997]: TR#153. State machine - state = CC_STATE_IDLE, event = EVT_ISDN_SETUP June 5 15:51:56.607 [3997]: TR#153): SC ...
3
votes
5answers
127 views

Get values block by block in same file

I have a file say "SAMPLE.txt" with following content, P1 10,9:6/123456 P2 blah blah P1 10,9:5/98765 P2 blah blah P1 blah blah P2 I want a output file say "RESULT.txt" as, Value1:123456 ...
1
vote
2answers
38 views

Reformatting a LaTeX document by perl

I have a LaTeX document in which the modifications in the text and equations are done in red color in order for them to be distinguished from unmodified text: {\color{red} MODIFIED TEXT OR EQUATION ...
2
votes
2answers
69 views

How to print top five highest numbers from a column?

I have a text file with four columns. I need to read till end of file and print the highest number from column3 (top 5 values) along with column 1. input.txt xm|340034177|ref|RT_235820.1| 139697 ...
1
vote
3answers
23 views

To bold one line with Perl regex

I have 1. Lorem He he he % not sure spelling 2. Lorem ipsun I want to have \textbf{1. Lorem} He he he % not sure spelling \textbf{2. Lorem} ipsun My pseudocode attempt perl -000pe ...
2
votes
3answers
103 views

Apply item replacement inside enumerate in Perl regex?

Data 7. Masi is the same as \begin{enumerate} A B ABC ha lorem \end{enumerate} 1. ABC is \begin{enumerate} P B Lorem maam \end{enumerate} which I want to be 7. Masi is the same as ...
4
votes
1answer
65 views

Regex this question format into LaTeX

1. Lorem ipsun la la la? 1. Sopor 2. Stupor 3. Torpor 2. A patient has Lorem? 1. Sopor 2. Stupor 3. Somnolentia 4. La 5. Coma 3. Doesn't Response to strong external irritants is short. Tendon, ...
1
vote
4answers
67 views

Remove only given strings from given column?

INPUT: <tr><td>FOOBAAR</td><td>FOOO</td><td>BAAR</td><td><font style=BACKGROUND-COLOR:red>2014-02-14 ...
1
vote
1answer
63 views

Using kornshell or Perl to circumvent permissions needed by root

I have a problem where I need to change the ownership and permissions of one file that exists on more than 200 servers. I belong to 2 different groups and need to change the ownership from one group ...
4
votes
7answers
323 views

How can I groups numbers in a file

I have a file with numbers in float format. I can review them via sort -rn numbers.txt | less I would like though to be able to "group" them. I.e. easily see how many are in the same range. To give an ...
1
vote
1answer
218 views

Perl print the lines matching with the columns of file 1 and file2

Here I am printing the contents of the file which are not matching. I want to do a vice versa, i.e. print the lines of file1 (those which are matching in file2) #!/usr/bin/perl # create names ...
0
votes
2answers
98 views

How to match date in Perl — assuming UNIX regex is the same as Perl's

I want to match dates of the form Monday May 26 My attempt to do this is the following: /(.*day Jan.*|Feb.*|Mar.*|Apr.*|May|Jun.*|Jul.*|Aug.*|Sep.*|Oct.*|Nov.*|Dec.* [1-31])/ The regex form in ...
4
votes
2answers
61 views

Using perl to modify a LaTeX document

I am trying to use perl in order to modify a LaTeX document. In fact, I am trying to change the citation format from for example: . \cite{poelma20113d} to \cite{poelma20113d}. In other words, I ...
3
votes
1answer
186 views

Interpret an interpolated variable as a literal string in Perl regex

I am using perl to colorize a matched string MATCH=aaa printf "aaa\n/dev/aaa\nccc\n" | perl -pe "s/($MATCH)/\e[1;31m\1\e[0m/g" This works well until I try to match a string containing special ...
2
votes
3answers
240 views

replace column of a csv file with column from another file

I have two sample files like this: $ cat file1 abc,sachin cat,kumar $ cat file2 xyz pressure $ cat file3 xyz,sachin pressure, kumar I want the first column of file1 to be replaced with file2. ...
0
votes
4answers
69 views

Print text between tags (inclusive) if certain text is found

I've got a task to extract data from several Apache servers. The task is to print out: <Directory ...> ... </Directory> where +ExecCGI is located within. Let me give an example to ...