Manipulation of text by programs, scripts, etc.

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0
votes
2answers
522 views

Add space after 8 characters then add space after every 4 characters

Here is the sample input: AbbigailAbieAbbyAbbi Using sed, I have separated them into 4 characters but seems like I got a problem because I have to separate the first 8 characters first then add ...
-1
votes
1answer
555 views

Match and combine records in Bash [duplicate]

Consider two csv files: $ cat given.csv 123,John 246,Paul 369,George 987,Ringo $ cat family.csv 246,McCartney 123,Lennon 987,Starr 369,Harrison Note that the lines are not ordered! How might I use ...
2
votes
5answers
160 views

Extract lines from a file containg From <str1> To <str2>

Let's says there is file "abc.txt" that contains a paragraph/lines: Hello, how are you doing sir? when are you going to arrive at the SBAHN platform to catch the train? How can I extract all the ...
2
votes
1answer
148 views

Comparing delimited fields

I have two fields in a file, students and teachers. They're delimited by a semicolon and I want to find which single students have two different teachers. jdoe;ateacher jdoe;bteacher jsmith;cteacher ...
0
votes
3answers
275 views

Combinatorics of letters and words - preferably bash, will accept perl or other [closed]

I am trying to write a shell script to generate all possible words in the English language less than 20 characters. I doubt there is any truly efficient way to do this other than to brute force some ...
0
votes
2answers
212 views

Convert two rows to two columns

I would like to convert every two rows to two columns using awk. Any help appreciated. input.txt: # Query: gi|11465907|ref|NC_001872.1| Chlamydomonas eugametos genome, complete genome # 0 hits found ...
1
vote
3answers
282 views

bash find using variable

I have an issue I don't understand. It is simple and it should work, but it doesn't. =EDITED exactly what I can see from terminal= I have a list of filenames: [molni@archlinux picasa_album]$ cat LIST ...
3
votes
3answers
358 views

Use AWK to pad date and time formats

I would like to use AWK to pad the date and time fields in my report. Here is my current .csv that is actually tab delimited. AA 9/7/2014 2:30:38 PM AA0000011111 08 Y A Jane, Doe AA ...
2
votes
2answers
29 views

Replace line names with set of new names without disturbing the rest of the file

I have a large protein sequence file where each sequence name is identified using > and the corresponding sequence in the following lines. Example (ignore quotation marks): >YAL003W EFB1 ...
-1
votes
3answers
706 views

How can I select columns based on a control file with invalid column numbers?

I have to generate the file dynamically from the source file based on the below control file. control_file.txt 1,3,5,-1,8,-1,4 The control file contains the position of columns which I require ...
6
votes
2answers
2k views

Compare two files and print matches

Is there anyway to get this through Unix shell scripting? I have a fileA with one column (1000 rows), and fileB with 26 columns(13000 rows). I need to search each value of fileA with fileB and return ...
1
vote
1answer
63 views

Create files from templates, substitutions in middle of other words

Is there a way to convince m4 to replace a macro in the middle of a word? I would like this file, day.m4: define(Sat,Cat)dnl Saturday and this command: m4 day.m4 to produce this output: ...
2
votes
3answers
193 views

Merging two tables including multiple ocurrence of column identifiers and unique lines

I asked a similar question yesterday (Merging two tables including multiple ocurrence of column identifiers) but ran into a problem with unique lines. I would like to merge two tables based on column ...
1
vote
3answers
82 views

Replace word instances with its count attached to it

I have a file which contains word 'name' multiple times ( 250 times ). I need to replace every instance of 'name' with its count attached to it as name_1, name_2, name_3....name_250. Can I do this ...
9
votes
7answers
14k views

Sed — Replace first k instances of a word in the file

I want to replace only the first k instances of a word. How can I do this? Eg. Say file foo.txt contains 100 instances occurrences of word 'linux' . I need to replace first 50 occurrences only.
2
votes
2answers
287 views

Merging two tables including multiple ocurrence of column identifiers

I would like to merge two tables: File 1: 1 today 2 tomorrow 3 red File 2: 1 a lot 1 sometimes 2 at work 2 at home 2 sometimes 3 new Desired output (file 3): 1 today ...
1
vote
2answers
1k views

Count the maximum character length for all the data fields in a simplified csv file and output to txt

Given a simplified CSV (max one line per row) with many data fields (>50), how can I count the maximum character length for each data field and then export all the counts to a txt file? BTW, I want to ...
1
vote
1answer
89 views

Take the subset of the file related to the time stamp

I have some json file in dictionary format. The lines looks like here: {"a":"1", "b":"2", "c":"3", "time":1334572551435} {"a":"1", "b":"2", "c":"4", "time":1334575352456} {"a":"2", "b":"2", "c":"7", ...
0
votes
2answers
37 views

How to find the occurrence of names in a file?

I want to know how many times users who have logged on the system in a single command. I have used repetitive commands to find the how many times he have logged. $ last | grep -c user1 $ last | grep ...
3
votes
3answers
2k views

sed match pattern N times

I want to split a file into chunks with 2 words each. $cat tmp word1 word2 word3 word4 word5 word6 word7 $sed -e 's/word. word. /&\n/g' tmp word1 word2 word3 word4 word5 word6 word7 $sed -e ...
3
votes
2answers
364 views

Outputting common lines from 2 files and uncommon lines from both the files in one output file

I have 2 text files. Lets name them file1.txt and file2.txt file1.txt is as follows chr10 181144 225933 chr10 181243 225933 chr10 181500 225933 chr10 226069 255828 chr10 255989 267134 ...
1
vote
1answer
178 views

Use case for /usr/bin/lessecho

I can not come up with an example of how I could/would use lessecho. The description in the man page is fairly straight forward but is not helping me come up with a use case: DESCRIPTION ...
1
vote
4answers
302 views

Decimal conversion number of the form x.xx to 0x.xx, sed?

I have a file of the form ... num 0.12 num num num 25.53 num num num 7.82 num num ... and I want to convert the 2nd field of each line adding a "0" at the numbers >= 0 and < 10 so the output ...
-2
votes
1answer
70 views

Place the cut field in the desired position of ouput file [closed]

I am writing a script like in which, it will cut the fields from input file and append to output file. cat $1|while read line do acc_no=`echo "$line" | cut -c29-43` acc_type=`echo "$line"|cut ...
-1
votes
1answer
48 views

convert scientific data into generic

I have a file containing only numerical values in scientific format. I want to convert them into generic notation and multiply them by 1000. e.g. input.txt 1.1234e-01 2.123e+01 3.12345e-02 ... ...
1
vote
1answer
89 views

Store output from one command and process it for another

I am working on Unix command line. I have two files. I want to cat file1.txt and grep the output in file2.txt File1.txt 123A 223A 143A 153A 183A 123J 123P File2.txt: 123A (TYU) 223A (RUT) 143A ...
1
vote
4answers
106 views

Parsing complex text file using Unix commands

I have the following text structure which I would like to parse: >Cluster 423 0 56aa, >HWI-ST1448:257:C3V2HACXX:1:1106:19087:2550.1... at 92.86% 1 64aa, ...
2
votes
3answers
708 views

how to concatenate a file with multiple header into one

Can you suggest me how I can combine. a.fasta with 10000 sequences having headers 1, 2, 3, .... 10000 .......................into just one header e.g >1 AAATTTTGGGGCCC >2 ACCCCGGGTTT ...
2
votes
0answers
69 views

Make GNU indent break long comments

Is there a way to convince GNU indent to break long comment and change it to multiline comment? Something like this: // Very long comment, longer than 80 characters. Just imagine that. To this: /* ...
0
votes
1answer
33 views

Print output of some my data in a file that should start with first line without blank space

By using some shell command i filter some output Please can some one suggest how i can print this output in some file For example I filtered some line and save it to some file but problem is it is ...
3
votes
2answers
494 views

awk: Extracting a fixed number of rows where the last row number may vary

This question may look like a duplicate, but only at first glance. Of course, I would no longer need help in how to code a one-liner that extracts a fixed number of continuous lines (e. g. 5 in this ...
1
vote
3answers
84 views

Print content of file from desired character and end also to desired character

I have this file with content written below. I want output of my file stating with ".SUBCKT C032_THS_COMPARATOR" and end with ".ENDS": .SUBCKT C032_THS_DPDNPROT_cdm_tdpdnw TOPROTECT VPLUS .SUBCKT ...
-2
votes
2answers
449 views

Grep and cut the selected field

I am trying to cut the field if a line starts with a particular name, cat $1|while read line do if [ "$1" = "custbills.cmp" ]; then acc_no=`grep "^Custbills" $1 | cut -c29-43` acc_type=`grep ...
5
votes
5answers
759 views

Replace data at specific positions in txt file using data from another file

I have a text file in the below format: $data This is the experimental data good data This is good file datafile 1 4324 3673 6.2e+11 7687 67576 2 3565 8768 8760 5780 8778 "This is line ...
3
votes
3answers
148 views

Replacing a pattern in line preceding another pattern of interest

I have a log file with many instances of statements as shown below: 14 Aug 19 16:30:11.506: <DATA> |POS|IDLE|1|01131844090|5950|$hostIp|$size |$data 20 Aug 19 16:30:12.439: <DATA> ...
5
votes
3answers
2k views

How to use awk through multiple files?

I want a solution for the general case (N folder) I'm using awk to process a file and extract its content and put it in a variable then echo it: This is the file: H1 H2 H3 H4 H5 H6 H7 H8 H9 not ...
2
votes
7answers
2k views

Adding a character to every other text line

I have a huge (ca. 20G) text file which contains millions of passages (a.k.a. paragraphs) with headers. Headers and paragraphs are always one line each, e.g., Sunshine This is a sunny day. ...
3
votes
2answers
119 views

Extract specific set lines matching a rule

I have a large file with the logs as shown below. There are about 30000 instance of such events logged. I need to extract those lines beginning with RINGING and CLOSE (included) and which does NOT ...
0
votes
2answers
96 views

Sum up the selected fields

I have a file with a numeric value in character positions 86 to 99. I want to sum up the entire amount present in the file, only for lines which contain RS at position 124-125. I am trying to do like ...
4
votes
4answers
75 views

stream edit >GDRLR5L04EQY8D 3931|1166 into >3931

I have large text DNA sequence files with the following format >name AACTGGGCT I need to parse the name line which currently has extra information and special characters, while keeping any line ...
2
votes
4answers
4k views

Error: ambiguous redirect while transferring output to command

Output to redirect in script: 511@ubuntu:~/Unix/test$ ls -ltr |awk '{print $9}' default.txt dfah.txt fruit.txt fruit_prices.txt dfh.txt header.txt testfile.txt topoutput.txt Script written on shell ...
4
votes
2answers
583 views

Compare 2 tab delimited files and output differences with column header

I would like to compare 2 similar files on a common column. The files will have identical headers. file1.txt mem_id Date Time Building aa bb cc dd ee ff ...
1
vote
3answers
349 views

cat a directories files apending the file name to the row of text and removing the header row? [closed]

How can I cat a directories files apending the file name to the row of text and removing the header row? So as to only have 1 header row in the all.txt file.
3
votes
3answers
2k views

Determine maximum column length for every column in a simplified csv-file (one line per row)

To determine the maximum length of each column in a comma-separated csv-file I hacked together a bash-script. When I ran it on a linux system it produced the correct output, but I need it to run on OS ...
4
votes
1answer
68 views

Truncated result returned by JOIN

I'm using join command under linux, but the results vary between different machines. I have two simple files: cat 1.txt a aaa,0.2 b bbb,0.3 c ccc,0.5 cat 2.txt a aaa,0.2 b bbb,0.3 c ccc,0.6 I'm ...
1
vote
4answers
95 views

Loop through array

I have records in list.txt (INPUT) as List of animals SET 1=Dog 2=Crow 3=Snake Pet,bird,reptile List of Countries SET 1=France 2=Singapore 3=Columbia Europe,Asia,SouthAmerica List of Parts SET ...
3
votes
3answers
3k views

Get the part of a line before the last slash

I'm trying to write a conky script that shows my MPD album art, a 'folder.jpg' in the album folder. My current plan is to use mpc -f %file%, which prints out the file name and path, and then cut out ...
1
vote
1answer
193 views

Why is the output of this paste command split on separate lines with indents?

I was trying to merge files using either of these commands: paste data_{1..2}.txt > 1_2.txt paste <(awk '{print $1}' data_2.txt ) <(awk '{print $1}' data_2.txt) > 1_2.txt But the ...
7
votes
7answers
22k views

How to find a position of a character using grep?

I need to identify the postion of a character in string using grep command. Example, the string is RAMSITALSKHMAN|1223333. grep -n '[^a-zA-Z0-9\$\~\%\#\^]' How do I find the position of | in the ...
4
votes
3answers
649 views

Replace “o” with “0” in large wordlist and save the original word?

I have a large text file with words. Every word is on a single line (typical wordlist). I want to replace all characters "o" with the number "0" in every word, and the new formed word to be pasted on ...