awk combine columns from multiple files

Hey Guys & Gals, Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Using AWK to merge two files based on multiple conditions, Using awk to print all columns from the nth to the last, Swap two columns - awk, sed, python, perl, Using an array in AWK when working with two files, Printing column separated by comma using Awk command line, awk search column from one file, if match print columns from both files, AWK comparing two files and printing individual columns. So . This is exactly what I need to be able to move forward. I have several column files like this I want to compare columns 1,2,4,5 from file 1 with columns 1,2,4,5 from file 2 and then merge matching lines in file 3 with column 3 of file 1 and all columns from files 2. cnvi0000003 5 165772271 0.3361 0 files_path="/home/###/###/people/" Short story taking place on a toroidal planet or moon involving flying, Difficulties with estimation of epsilon-delta limit proof. I have tried various combinations of merge, lapply, rbind, join, etc. How do I copy a folder from remote to local using scp? Difference between "select-editor" and "update-alternatives --config editor". my $index = @if; A while ago I stumbled in a very good solution to handle multiple files at once. Asking for help, clarification, or responding to other answers. I found this question/answer on Google and it appears to be referring to a very specific data set found in another question (How to merge two files using AWK?). (sorry about word wrap) -- Sired, squired, hired, RETIRED. So, the command above joins the files on the second field and prints the 1st,2nd and 3rd field of file one, followed by the 3rd field of file2. one file unit accessing two different files. 5 165772271 0.4321 0.2955 0.3361 Did this satellite streak past the Hubble Space Telescope so close that it was out of focus? How can I sum values in column based on the value in another column? when cating you need to ensure the file order is preserved, one way is to explicitly specify the files, extract last column by awk and align using pr, Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Find centralized, trusted content and collaborate around the technologies you use most. #!/usr/bin/env ksh and what would happen then? my $str = ""; # build the infoline here s1 s2. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 1wert It is just the combination of the 2 columns that is unique in each of the whole files. Search for jobs related to Extract data from log file in specified range of time awk or hire on the world's largest freelancing marketplace with 22m+ jobs. Minimising the environmental effects of my dyson brain, Follow Up: struct sockaddr storage initialization by network format-string. Ubuntu and the circle of friends logo are trade marks of Canonical Limited and are used under licence. The first is the row function and the column function, and their functions are to return the row number and column number of the cell respectively. name Chr Position Log R Ratio B Allele Freq missing_snp = NULL x[FNR] = $0 I have many files formatted like this: My goal is to have a column from the 2nd file placed inbetween the columns in the first file. It concatenates each full line from the first file with the corresponding line from the second file; you can remove unwanted columns before or after. Data_a2 Why is there a voltage on my HDMI and coaxial cables. Create File in Linux. I use that feature to enable plotting of data from two datafiles in one. 1) create a dummy field from the desired columns of file A or B. I need to join file2 to file1 when column 3 in my file1 and column 1 in my file2 in the same string By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. That was the problem. For example, assuming that your columns are tab-delimited: paste file1.txt file2.txt | cut -f 1,2,3,6. } I want to compare columns 1,2,4,5 from file 1 with columns 1,2,4,5 from file 2 and then merge matching lines in file 3 with column 3 of file 1 and all columns from files 2. I added an extra line to the sample data containing: The output I got from that plus the data in the question looked like this after formatting with tabstops set to 4: Very similar to @sps answer but without the if and using tabs. File: a.txt For example : 1) awk 'BEGIN{FS=OFS=","}NR==FNR{a[$1$2$4$5]=$3;next} $1$2$4$5 in a{print $0, a[$1$2$4$5]}' file2 file1 > file3 2) awk 'NR==FNR {a[$1$2$4$5] = $3; next} $1$2$4$5 in a' file2 file1 >file3 [duplicate]. if ( defined ( $if[$index]->{handle} ) and $if[$index]->{F}[0] == $pos ) { $if[ $index ]->{ F }[0] = -1; # set default pos value for this file to "unread" Hi all, I searched through the forum but i can't manage to find a solution. Works fine - but quoting gets a bit tricky, when I call. cnvi0000001 5 164388439 0.2449 0 > 5 > 6 > 7 > 8 > into one file to give, awk '{printf "%s ",$0;getline < "file2";print $0}' file1. } llr[$1]="\t"; file2 Merge selected columns from two different files into another file. I hope at least that this inspires you all to take advantage of the power of AWK! tot_file <- read.table(files[1], sep="\t", header=TRUE)[c(1,2,3)] The way is to save in memory the files in AWK arrays using the method: FILENAME==ARGV [1] { file2array [FNR] = $0 ; next } FILENAME==ARGV [2] { file1array [FNR] = $0 ; next } UNIX is a registered trademark of The Open Group. This will help others answer the question. File1_example.txt. But it still leaves out one semicolon--or a column--from output lines 1 and 4: An how do I state which columns I want to use for comparing? Why did Ukraine abstain from the UNHRC vote on China? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded. 20130322 05:35 2219 A1BG 3 Without messing up the elements orders of BOTH files. Home: Forums: Tutorials: Articles: Register . cnvi0000002 5 165771245 0.4448 1 here we handle the 1st input (file2). For example: awk ' {print NR,$0}' employees.txt. Table5|Column4 When using awk, you can specify certain columns you want printed. Is the God of a monotheism necessarily omnipotent? Trying to understand how to get this basic Fourier Series. 2tg Making statements based on opinion; back them up with references or personal experience. Browse other questions tagged. The paste command can merge lines of multiple files. $ cat file2 3) sort the output for usability with join. input1 } if so, either convert them to Unix style (with. The problem I'm having is I need to only combine data from the second file in the empty spaces of the first. I was trying to delete line endings for each files first (tr 'r' 'n' < file1 > file1new) before applying awk command. Arrays in awk are associative and is a very powerful feature. AA|RR|ESKIM|ES But changing the awk record directly was definitely the solution. The files are experiment results with columns of data separated by white space. } ax200 2 3 4. Is there a single-word adjective for "having exceptionally strong moral principles"? Try this: awk '{sub("#*","");printf "%s ",$0;getline < "file2";sub("#*","");print$0}' file1. if ( defined ( $if[$index]->{line} = <$handle> ) ) { PDB CHAIN Start End Fragment 4asdf What is the purpose of this D-shaped ring at the base of the tongue on my hiking boots? done, paste $f0 ${f0%. The join command joins the lines of two files which share a common field of data. Awk command performs the pattern/action statements once for each record in a file. xx_file_noname <- cbind(xx_file$Position, xx_file$Log.R.Ratio) Styling contours by colour and by line thickness in QGIS. Step 1: NR==FNR { out [$1]=1; next } awk reads the first line from the first file lines_to_show.txt, which is: 2. How Intuit democratizes AI development across teams through reusability. ------------ This may look very untidy but should work. Short story taking place on a toroidal planet or moon involving flying. I want to extract and combine a certain column from a bunch of text files into a single file as shown. The case where there's an odd number of fields on the line doesn't need special treatment. Busca trabajos relacionados con Extract data from log file in specified range of time awk o contrata en el mercado de freelancing ms grande del mundo con ms de 22m de trabajos. How do you ensure that a red herring doesn't violate Chekhov's gun? Can I tell police to wait and call a lawyer when served with a search warrant? cnvi0000002 5 165771245 -0.0163 1 Input File: Hi, By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. cnvi0000004 5 166325838 0.0307 0.9867 4. In our case here, we use only the index without values. e I think awk code is more easily understood when formatted using multiple lines for multiple statements. file2.csv: How can I merge two contiguous columns, say the 2nd and the 3rd, to get, I need the code to work with text files with different numbers of columns, so I can't use something like awk 'BEGIN{FS="\t"} {print $1"\t"$2"-"$3"\t"$4"\t"$5}' file. I have 2 files. 5 166325838 0.0403 -0.118 0.0307 1avq A 171 176 awyfan rev2023.3.3.43278, Not the answer you're looking for? use warnings; Join 2 files with multiple columns: awk/grep/join. print p[i] I want the 1st and 2nd columns which are the same in all the files and 4th column which is different in all the files. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 1/2-SBSRNA4 53 You can convert these 5 columns of data into 1 column for display. @EdMorton : You've just made a good point.. File 2 has entries missing for some date time. Identify those arcade games from a 1983 Brazilian music video. Lot's of tweaks could be made to this script; for instance, adding trap statements to clean up the temporary file in the event of a signal, adding checks for the appropriate number of arguments to the script, a function for running the sed | awk part of the pipeline, etc. When NR != FNR it's time to process 2nd input, file1. file1 cnvi0000003 5 165772271 0.2955 0.0042 Why do small African island nations perform better than African continental nations, considering democracy and human development? Relation between transaction data and transaction id, Equation alignment in aligned environment not working properly. cnvi0000005 5 166710354 0.1529 0, chr Position File1 File2 File3 how to add zero if two columns are not in length? # print the header after all the other columns from file A. I have found several examples here in SO (for example How to merge two files based on the first three columns using awk and How to merge two files using AWK?) Merge multiples files with multiples duplicates keys by filling "NULL" the void columns for anothers joinning files desired put put if(llr[$1]){ # add missing values for my $index ( 0 .. $#if ) { rev2023.3.3.43278. How to use awk to extract the required columns and create a new file? cnvi0000001 5 164388439 -0.4241 0.0097 ax100 10 20 40 Possible approaches: I would suggest the following approaches instead of trying to use MERGE statement within Execute SQL Task between two database servers.. The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup, Pick columns from a variable length csv file, How to compare 2 files with common columns and then get the output file with columns from each file. Here's a way to pre-filter both files that relies . rev2023.3.3.43278. xx_file <- read.table(files[i], sep="\t", header=TRUE)[c(1,3,4)] Table2|Column1 The best answers are voted up and rise to the top, Not the answer you're looking for? else { 6. Awk can take the following options: -F fs To specify a file separator. c. Hi Friends, Could anyone help me with this issue ? else { ax200 12 13 44 1430,Aircel MP,20 (separating the fields with FS i the associative array key string just guards against false matches; if you just concatenate fields you can't distinguish between "abcdef" and "abc""def"). e Not the answer you're looking for? I still get empty output. Using Kolmogorov complexity to measure difficulty of problems? cnvi0000004 5 166325838 0.0307 0.9867 ax100 20 30 40 Right side: line #1 I am line 2 on the left. 1. 5 164388439 -0.4241 0.0736 0.2449 Seems that working. print "$$ref[1]\t$$ref[2]$str\n"; 5 166325838 0.0403 -0.118 0.0307 -0.118 -0.118 0.0307 How to to create a new file with specific columns from files in multiple folders in linux? Thanks to all of you that got me started into awk. Thank you very much. 5 165771245 0.4448 0.1811 -0.0163 Data_c4 It is relatively expressive and easy to understand. communities including Stack Overflow, the largest, most trusted online community for developers learn, share their knowledge, and build their careers. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Why do we calculate the second half of frequencies in DFT? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. The above was run using this input (all spaces are tabs): To subscribe to this RSS feed, copy and paste this URL into your RSS reader. awk not merging two files based on the matching of two columns, Linear regulator thermal information missing in datasheet. Having issues trying to get the columns to format properly. *}.m, 10 More Discussions You Might Find Interesting. In my book, 'one-liner' is a term of abuse unless the code fits on a single line under about 80 characters. Each file has 3 columns (2 other columns in addition to the first common column). I'm almost correct in doing it. # character and position later Do roots of these polynomials approach the negative of the Euler-Mascheroni constant? Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? *//' $2 | awk 'NF > 0 {print $2}' | paste tmp.$$ - rm -f tmp.$$ ---. It has more code, but if you want more complex data treatment, I think it's the better approach. How can I check before my flight that the cloud separation requirements in VFR flight rules are met? In "Merge into", select the completed "Merged into file.xlsx" 5. To learn more, see our tips on writing great answers. Let's analyze this formula with you. I tried to use bold in it but it doesn't work in code block. Not the answer you're looking for? Anyway - maybe somebody feels the same about gnuplot, which I really do like, just missing this feature. Table2|Column5 Output I would like to merge multiple columns into one column, for example, Review your favorite Linux distribution. 1|def How do you ensure that a red herring doesn't violate Chekhov's gun? By the way, if there is any good website for an awk command tutorial, please recommend it here. I want to use awk to combine columns starting from 4th column till the end of columns. Browse other questions tagged. How to join files with required columns in linux? Also, it's pretty easy to use: $ paste left.txt right.txt I am line 1 on the left. 3. chr Position Code: pr -m -t -s\ file1 file2 | gawk ' {print $4,$5,$6,$1}'. 1. All these. AA|RR|ESKIM Minimising the environmental effects of my dyson brain. What is the purpose of non-series Shimano components? 2tg 2|ghi Minimising the environmental effects of my dyson brain. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Data_c2 c - Insert Data What sort of strategies would a medieval military use against a fantasy giant? It only takes a minute to sign up. if ( -r $_ ) { Table4|Column3 5 164388439 -0.4241 0.0736 0.2449 As we read lines from file all_lines.txt, we print the line if the current line number exists in the array. Join multiple files by column with awk. > > -- > > Sired, squired, hired, RETIRED. We will see how to process files and print results using awk. input4 Then from the command line, I try to print the first, second and third fields from the file tecmintinfo.txt using the command below: $ awk '// {print $1 $2 $3 }' tecmintinfo.txt TecMint.comisthe. Is it correct to use "the" before "materials used in making buildings are"? Why do academics stay as adjuncts for years rather than move around? a Home: Forums: Tutorials: Articles . > Hm - Is there a way of just reading in rows without that key? 5asdf So far I've assumed that you want to match line 1 of file 1 with line 1 of file 2, line 2 of file 1 with line 2 of file 2, etc. 5 166325838 0.0403 -0.118 0.0307 END{for(i in p) { Making statements based on opinion; back them up with references or personal experience. 2|jkl Judging from the data layout in the question, tab separators were used in the original data, but the presentation is with tabstops set at 4 spaces. } END { How to delete from a text file, all lines that contain a specific string? I have two files I need to combine. Actually i did try to specify the separator but i get the same result. File2: b.txt How can I recursively find all files in current and subfolders based on wildcard matching? Is it correct to use "the" before "materials used in making buildings are"? Visit Stack Exchange Tour Start here for quick overview the site Help Center Detailed answers. Counts the number of fields in the current input record and displays the last field of the file. Awk spilt each line in the file into fields using the field separator values and stores them in incrementing references, $1 being the first field, $2 the second ect. To learn more, see our tips on writing great answers. tot_file_noname = cbind(tot_file_noname, xx_file_noname[,2]) could you be more specific in terms of Input, desired output, how the (and which) columns should be compared? If you preorder a special airline meal (e.g. } Oh, I skipped that you want the unmatched lines of, Using AWK to merge two files based on multiple columns, How to merge two files based on the first three columns using awk, How Intuit democratizes AI development across teams through reusability. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). chomp; ------------ Apparently now it's only using first column for comparing. }else{ } s[$1] = s[$1] " " $4; you could man gawk check what are NR and FNR{ print $0, a[$1]}' file2 file1 . What sort of strategies would a medieval military use against a fantasy giant? rev2023.3.3.43278. Connect and share knowledge within a single location that is structured and easy to search. How to tell which packages are held back due to phased updates. Combine text from two files, output to another [duplicate], How Intuit democratizes AI development across teams through reusability. # write the "big" file For example : awk 'BEGIN {FS=OFS=","}NR==FNR {a [$1$2$4$5]=$3 . Exemple: File 3 may contain column 1,2,3 from File 1 and column 4 from File 2. How to create a new file merging selective columns from two separate files using awk? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video, Linear Algebra - Linear transformation question. I have a large number of files (say X) each containing two columns of data and the same number of rows. The files begin with several lines of header which are all preceeded by a comment character '#'. my $dummy_fh = $if[ $index ]->{ handle }; By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. I wanted to see how it could be done with. I saw some suggestions to use pr/paste to join the columns and then awk to pick-up the columns. Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. 5678,GHIJ,24,TOM,NY,USA 1c7k A 2 7 awk, columns, files, join, linux, merge, script, shell scripts, sql, Join columns across multiple lines in a Text based on common column using BASH, bash awk, bash command, loop in awk, shell scripts, solved, http://www.unix.com/shell-programminple-files.html, http://www.unix.com/shell-programminping-file.html, Join, merge, fill NULL the void columns of multiples files like sql "LEFT JOIN" by using awk, Awk: Multiple Replace In Column From Two Different Files, How to use the the join command to join multiple files by a common column, Join multiple files based on 1 common column. #I add them in the current xx_file object with value "NaN" 5asdf 1/2-SBSRNA4 18 5 166710354 0.2355 0.1529, awk '{ I'm trying to combine all the second columns ($2) together. The closest solution I could get to, is the following Merge files using a common column However, . a How to concatenate multiple columns with colon sign using awk? cnvi0000002 5 165771245 0.1811 1 print('different!') The files are named GSM1.txt through GSM20.txt. input3 inefficient code: comparing combining different columns from different files awk or perl? Data Field Of course I don't mind :) I'm glad my answer helped you too. Making statements based on opinion; back them up with references or personal experience. I have 3 files with one column value as shown I have n files (for ex:64 files) with one similar column. I have a file1 with 3400 records that are tab separated and I have a file2 with 6220 records. Can carbocations exist in a nonpolar solvent? } What sort of strategies would a medieval military use against a fantasy giant? $ cat file3 }, 10 More Discussions You Might Find Interesting. Data Field It worked once when joining on individual columns but is not working with two. FILE1 for (i in 1:length(files)) { if (length(xx_file$name) != length(tot_file$name)){ Thank you. merge columns from multiple files. Styling contours by colour and by line thickness in QGIS. Kent, excellent explanation; thank you very much. paste $f0 $f1 | awk '{print $1, $5}' >${f0%. but i'm getting empty output. Hello, I am not sure if it is reposted, but I could not find the same thread. I want to merge columns (selectively) from several files and create a new file with the merge output. missing <- data.frame(Position = tot_file[i,]$Position, Log.R.Ratio="NaN") d Share. awk '{print $1"\t"$2}' file # OR awk '$1 = $1' OFS="\t" file 03-14-2012, 11:45 AM #6: David the H. Bash Guru . Do roots of these polynomials approach the negative of the Euler-Mascheroni constant? @sjsam I always recommend people buy the book instead of suggesting they read it for free online as the guy who wrote it deserves to make a few bucks off that plus all the work he's put into providing and maintaining gawk for us and shouldn't be penalized for graciously also providing it online for reference. How to compare two columns from two different files? Edit the question to include desired behavior, a specific problem or error, and the shortest code necessary to reproduce the problem. use strict; 3|pqr File is sorted by ColumnName. Data_b3 Thanks for contributing an answer to Stack Overflow! SUPSS|SS } Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. cnvi0000001 5 164388439 -0.4241 0.0097 -- Eat Healthy | _ _ | Nothing would be done at all, 2345,ABCD,24,SAM,NY,USA []how can i get certain columns and certain rows from file with egrep and awk 2014-05-30 10:50:35 5 86 linux / bash / awk / grep. for ( 0 .. $#if ) { Learn more about Stack Overflow the company, and our products. 5 165771245 0.4448 0.1811 -0.0163 To have the first column printed, you use the command: awk ' {print $1}' information.txt. The best answers are voted up and rise to the top, Not the answer you're looking for? } The command displays the line number in the output. @{$if[$index]->{F}} = split(/\s/, $if[$index]->{line}); #load files to create the "complete list" I need the first column that contain the name of the record Ouput: Thomas Omega Wood Giorgos Timmy. Implement Seek on /dev/stdin file descriptor in Rust, Difference between "select-editor" and "update-alternatives --config editor", Doesn't analytically integrate sensibly let alone correctly. print "\n"; here we print the line of file1 . Why did Ukraine abstain from the UNHRC vote on China? Is it possible to rotate a window 90 degrees if it has the same length and width? c How to use Slater Type Orbitals as a basis functions in matrix method correctly? $cat a_b_s1.xls What is the point of Thrower's Bandolier? > > awk '{printf "%s ",$0;getline < "file2";print $0}' file1. Try that when the input file contains a line that starts with, say, %s. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Merge selected columns from two different files into another file. How can I check before my flight that the cloud separation requirements in VFR flight rules are met? b - Insert Data Though you could probably use some UNIX utilities like join or paste, AWK is obviously much more flexible and powerful if your desired output is different, by using if statements, or altering the OFS (which may be more difficult to do depending on the utility; see below) for example, altering the output in a much more expressive way (an important consideration for shell scripters.