1
vote
4answers
103 views

Sed/awk/perl: reversing order of comma separated values, preserving other text

I have this text: LABEL1 .BYTE 01, 02, 03, 04, 05 .BYTE 01, 02, 03 I need to reverse only comma separated values order: LABEL1 .BYTE 05, 04, 03, 02, 01 .BYTE 03, 02, 01 I need ...
1
vote
1answer
33 views

count matches and mismatches group by

Please help with a shell script of the following. I need count number of consistent variables in each lane (col1) across samples (col2). For example, since all the values (col4) of lane1 variable 1 ...
2
votes
2answers
35 views

Sed/awk/perl: modify text preserving parts and align to a column

I have a text like this: A1JOURNEY0TO1 .BYTE 00, 00, 00 A2JOURNEY0TO2 .BYTE 00, 01, 00 A3JOURNEY1TO0 .BYTE 00, 01, 01 I need to have: JOURNEY_01 ; 00 TO ...
-1
votes
1answer
38 views

How to remove only 0-9 character long numbers from a file?

How can we remove only the numbers that are 0,1,2,3,4,5,6,7,8,9 character long from a file? I mean the lines that are matching this pattern. Example for removable lines: cat input.txt 1 123423113 ...
0
votes
1answer
55 views

Cut a specific part of a column from a csv file [closed]

I have to process a csv containing about 15 columns one of which contains a particular timestamp that includes milliseconds. When I go to insert this csv into a DB, I get an error because of this ...
2
votes
1answer
90 views

grep search expression and rename file

I have readable pdf files that all contain the string VAX followed by eight numbers, like VAX00002885. Now I want to find that expression and rename the corresponding pdf to VAX00002885.pdf (in this ...
0
votes
5answers
43 views

df -k + how to match the root volume line

please advise how to match the "/" volume from df -k command? I tried the following: [root@machine /]# df -k | grep "/" /dev/vx/dsk/bootdg/rootvol 130926685 71378710 58238709 56% / /devices ...
-1
votes
1answer
33 views

search for a character in one column and replace value in another column of matched records

I have a requirement to find value 2 in column 4 and wherever it matches replace 6th column with '-'sign in the beginning suppose if i have csv file - file1 like this abc,0,def,1234,ijk ...
0
votes
3answers
45 views

How to Print certain Fields if a condition is met

I have a big Input file as shown below. If "PRIMER_LEFT_NUM_RETURNED" is not equal to 0 then print the corresponding SEQUENCE_ID, SEQUENCE_TEMPLATE,PRIMER_LEFT_NUM_RETURNED, PRIMER_RIGHT_NUM_RETURNED, ...
3
votes
3answers
278 views

Replacing string in all files found by grep. Can't get it to work

I'm trying to do what title says. So I find all needed files with grep: grep --include=\*.{php,ini,conf,sh} -ril -P "'([\d\w\-\_\.]+)(@domain.com)'" '/var/www_data/somepath/' Now I assume it's ...
3
votes
4answers
51 views

Need to remove - (Minus) sign at the end in number from many columns and insert it on columns removed

I have a huge csv file which has - (Minus) sign at the end of numbers. Now I need to move these - minus signs to begin of the numbers, i.e I need to remove the last character if it has '-' sign and ...
1
vote
3answers
36 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 ...
2
votes
3answers
34 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
2answers
227 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
285 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 ...
1
vote
1answer
51 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). ...
1
vote
4answers
79 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 ...
2
votes
3answers
640 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
78 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 ...
0
votes
2answers
98 views

Method to paste specific column when in terminal

I'd like to paste only the third column of data from within the terminal. I originally have something like: 4 SF0086 SF0086 12 SF0087 SF0087 17 TSF141 TSF141 29 TSF070 TSF070 30 TSF028 TSF028 31 ...
4
votes
7answers
331 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
3answers
79 views

Are there any difference using pipes?

Using Ubuntu 12.04. Using pipes (5 times): $ time echo XYZ | sed 's/X/A/g' | sed 's/Y/B/g' | sed 's/Z/C/g' ABC real 0m0.005s user 0m0.000s sys 0m0.000s $ time echo XYZ | sed 's/X/A/g' | sed ...
1
vote
3answers
1k views

Extract part of string using grep

I have 3 files in a directory MYO144064T MYO144064TA MYO144064TX Where the digits and 11th character will change. In my csh script, I want to extract the letters 'A' and 'X' probably using grep ...
4
votes
4answers
146 views

How to switch the first letters of two words?

$ echo 'foo bar' | sed SOMEMAGIC boo far $ echo 'one two' | sed SOMEMAGIC tne owo Q: in general, how can I replace the "b" from the "bar" to the "f" of the "foo"? And in reverse too, replace the "f" ...
1
vote
3answers
447 views

Print the last-but-one field

How to print the word before the last word in line (with ksh or awk or sed or perl one liner) Example 1: echo one two three will print "two" Example 2: echo 1 2 3 4 5 6 will print "5"
0
votes
2answers
87 views

search for first pattern and copy the string inside the ( ) into the 3rd field in lines where the second pattern found

Here are my spec: first search for "#firstpattern(" copy the content inside the ( ) to the 3rd field inside the ( ) of all lines where the "secondpattern" found. remove the entire line with the ...
3
votes
2answers
338 views

case sensitive substitution; same target ids

I am struggled myself to make a case sensitive replacement in a text file. Please find below a segment of my sed file that I am running as sed -f file.sed < input.txt > output.txt ...
2
votes
5answers
252 views

Can the string “abcedf” be matched to string “bafcde” in a single line command?

I am planning to implement an indexing structure in my program. For example, if I have 100 rows in the table, I will number these rows from 1 to 100 in another column by appending an _ to the end of ...
1
vote
4answers
545 views

Pattern Matching and Delete the whole line

I want to delete all the Lines of File 1, if Column1 of File1 matches exactly with Column 1 File2. File 1: r001:21:10 21 AAAAAATTTGC * = XM:21 r002:21:10 21 YAAAATTTGC * ...
4
votes
2answers
653 views

Replace string with sequential index

Can someone suggest an elegant way to accomplish this? Input: test instant () test instant () ... test instant () //total 1000 lines output should be: test instant1 () test ...
6
votes
2answers
2k views

Remove unknown unicode character from textfiles - sed, other bash/shell methods

I need to search and replace all occurences of an unknown character in some files having the same name. Opening such files with vi, I read <91> code for that character. Opening them with nano, I ...
1
vote
1answer
119 views

pcregrep fails due to segmentation fault

I am extracting the HTML source of a web page using the below command. curl http://www.linkedin.com/pub/ramesh-venkataraman/63/621/b42 -s | w3m -dump -T text/html > foo.txt The foo.txt has the ...
3
votes
3answers
2k views

extract only the substring after double quotes - grep

I have a file which is as below. <a href="http://firstlink.com" title="title1"> <a href="http://secondlink.com" title="title2"> <a href="http://thirdlink.com" title="title3"> <a ...
3
votes
1answer
116 views

Reorder Multiple Line Blocks with Sed

I am trying to reorder generated output as follows; given a tex fragment as follows, I want to move the /^Constant/ down below /Dummies/, with the line before and after /^Constant/. Further, I would ...
-2
votes
3answers
95 views

Deleting Lines, which match a particular Identifier from another file

I have 2 files. File 1, has an identifier (eg. D7MHBF:11:1449:1988) and every new entry starts with @. It has few more fields, which are not important in our analysis. File 2 consists of a column of ...
15
votes
1answer
8k views

How can I replace a string in a file(s)?

Replacing strings in files based on certain search criteria is a very common task. How can I replace string foo with bar in all files in the current directory? do the same recursively for sub ...
0
votes
2answers
64 views

Turning percentages into decimals?

I've got a CSV file that has percentages here and there expressed in text format, e.g. 173.91,0.00%,36.10%,1.71 Question of the day is how do I turn that example into 173.91,0,0.3610,1.71 Edit ...
1
vote
1answer
143 views

Parsing csv with sed and perl one-liner?

I have a web server which stores configurations to PostgreSQL, and I plan to retrieve information from a certain table and then later parse it into csv format. PAYLOAD <?xml version="1.0" ...
2
votes
4answers
234 views

Print the string between two parentheses

I have file with these lines G8 = P(G1,G3) G9 = P(G3,G4) G12 = P(G2,G9) G15 = P(G9,G5) G16 = P(G8,G12) G17 = P(G12,G15) I need the output as G1,G3 G3,G4 ..... How can I do it with sed/grep ...
0
votes
1answer
38 views

rearranging from colum to row in a csv [duplicate]

I have a CSV file that presently has an output like this 1 2 3 4 5 what I need to do is reconfigure the output as follows 1 2 3 4 5 all the entry data on one line, any help would be greatly ...
0
votes
1answer
127 views

best programming language for I/O intensive tasks [closed]

I need to process "big data" (nearly 1TB which can be partitioned into smaller chunks). Consider several programming languages (Java, Python, C++, Perl) and other scripting options (Perl, awk, sed, ...
4
votes
6answers
101 views

Only show the lines that are in all textfiles at least once

a.txt cat a.txt a b x c b.txt cat b.txt d e a f the q: SOMEMAGICK *.txt a Q: how can I show only the lines that are in all *.txt files?
3
votes
3answers
4k views

importing data from a text file to a bash script

I need to import a text file like this below: AMBI CBNK CCXI CERE CLACW CNYD DAEG DLIA DLLR DNDN DSGX HAST HIBB, HPOL IRDMZ MARK NEPT NFEC NINE NRCIB OMER PLCC PLPM PSUN UNTK There are 25 entries, ...
1
vote
3answers
541 views

How to limit MAX an MIN length of a string?

"nothing" means no OUTPUT. Q: how can I limit the MIN and MAX length of a piped STRING? (MIN: x>=3 chars, MAX: x<=32 chars) INPUT: echo 12 | MAGIC OUTPUT: nothing INPUT: echo 123 | ...
1
vote
1answer
53 views

How to make URL's out of this text with least resources?

INPUT: nyeeeeeeeeeeeeeee.txt:sadfsadf sadjflsajfd:jasdlfjalsfd foo/asdfsafd.txt:laksjdlfajsfd OUTPUT: <a href="nyeeeeeeeeeeeeeee.txt">nyeeeeeeeeeeeeeee.txt</a>:sadfsadf <a ...
5
votes
1answer
199 views

Execute a command within 'sed'

I have a list of random memory addresses saved in a text file, and I need to sed them out, decode them, and save them back to my file. However, the decoding operation I'm trying to perform is handled ...
2
votes
6answers
3k views

Repeat each line multiple times

Would like to have each line in a file repeated a fixed number of times. e.g. have each line repeated four times: a b c becomes: a a a a b b b b c c c c I've done some searching, and there are ...
2
votes
2answers
156 views

linux & solaris - separate netmask IP's from ordinary IP's

I have file with IP address and netmask IP's my target is to cut the netmask IP's from the file_with_IPs.txt and paste them to another file as file_with_only_netmask_ips.txt remark - netmask IP can ...
-3
votes
4answers
661 views

perl one liner + how to replace any last IP address octets

How to replace any last IP address octets (four octet ) to 0 remark: Implementation should be by Perl one linear on linux machines for example 192.9.200.124 will replaced to 192.9.200.0 ...
2
votes
3answers
1k views

I want to find duplicates in a file and add a character to the end of the line on the 1st match

I am trying to find duplicates in a file and once a match is found mark the 1st match with a character or word on the end of the line. eg my file (test.html) contains the following entries host= ...